[English] 日本語
Yorodumi
- PDB-4dr6: Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dr6
TitleCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound
Components
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
  • 5'-R(*UP*UP*U)-3'
  • 5'-R(*UP*UP*UP*U)-3'
  • 5'-R(P*CP*UP*UP*GP*AP*GP*GP*(PSU)P*GP*GP*U)-3'
  • 5'-R(P*UP*UP*GP*AP*GP*GP*(PSU)P*GP*G)-3'
KeywordsRIBOSOME/ANTIBIOTIC / decoding / Streptomycin / RNA structure / antibiotic resistance / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain ...S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Ribosomal protein S3 C-terminal domain / Ribosomal protein S6/Translation elongation factor EF1B / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / S15/NS1, RNA-binding / Helix hairpin bin / Ribosomal Protein S7 / Ribosomal protein S7/S5 / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Ribosomal protein S14, type Z / Double Stranded RNA Binding Domain / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S14/S29 / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Few Secondary Structures / Irregular / K Homology domain / K homology RNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Nucleotidyltransferase; domain 5 / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily
Similarity search - Domain/homology
STREPTOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...STREPTOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.3 Å
AuthorsDemirci, H. / Murphy IV, F. / Murphy, E. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
CitationJournal: Nat Commun / Year: 2013
Title: A structural basis for streptomycin-induced misreading of the genetic code.
Authors: Demirci, H. / Murphy, F. / Murphy, E. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
History
DepositionFeb 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Feb 19, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S rRNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein THX
V: 5'-R(*UP*UP*UP*U)-3'
W: 5'-R(P*UP*UP*GP*AP*GP*GP*(PSU)P*GP*G)-3'
a: 5'-R(P*CP*UP*UP*GP*AP*GP*GP*(PSU)P*GP*GP*U)-3'
b: 5'-R(*UP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)802,309404
Polymers792,45825
Non-polymers9,851379
Water16,340907
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)402.600, 402.600, 174.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
RNA chain , 5 types, 5 molecules AVWab

#1: RNA chain 16S rRNA


Mass: 494170.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: M26923.1
#22: RNA chain 5'-R(*UP*UP*UP*U)-3'


Mass: 1179.706 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: mRNA A Site / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#23: RNA chain 5'-R(P*UP*UP*GP*AP*GP*GP*(PSU)P*GP*G)-3'


Mass: 2928.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ASL (Leucine 2) A Site / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#24: RNA chain 5'-R(P*CP*UP*UP*GP*AP*GP*GP*(PSU)P*GP*GP*U)-3'


Mass: 3540.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ASL (Leucine 2) Shine Dalgarno mini helix / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#25: RNA chain 5'-R(*UP*UP*U)-3'


Mass: 873.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: mRNA / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8

-
30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S ribosomal protein S2


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371
#3: Protein 30S ribosomal protein S3


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372
#4: Protein 30S ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373
#5: Protein 30S ribosomal protein S5


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5
#6: Protein 30S ribosomal protein S6


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8
#7: Protein 30S ribosomal protein S7


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291
#8: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#9: Protein 30S ribosomal protein S9


Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374
#10: Protein 30S ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7
#11: Protein 30S ribosomal protein S11


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376
#12: Protein 30S ribosomal protein S12


Mass: 14966.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: F6DEQ7, UniProt: Q5SHN3*PLUS
#13: Protein 30S ribosomal protein S13


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#15: Protein 30S ribosomal protein S15


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76
#16: Protein 30S ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3
#17: Protein 30S ribosomal protein S17


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#18: Protein 30S ribosomal protein S18


Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0
#19: Protein 30S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2
#20: Protein 30S ribosomal protein S20


Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein THX


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

-
Non-polymers , 4 types, 1286 molecules

#26: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 376 / Source method: obtained synthetically / Formula: Mg
#27: Chemical ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A


Mass: 581.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H39N7O12 / Comment: antibiotic*YM
#28: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#29: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.49 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 6.5 / Details: MPD, pH 6.5, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2011
RadiationMonochromator: double crystal Si(111) monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionNumber: 2412927 / Rmerge(I) obs: 0.092 / D res high: 3.3 Å / Num. obs: 213602 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
14.7650256796.510.03
10.4414.76458210010.035
8.5210.44584710010.039
7.388.52682910010.044
6.67.38769410010.049
6.026.6846610010.058
5.586.02920910010.063
5.225.58983610010.07
4.925.221046910010.078
4.674.921102010010.091
4.454.671159710010.105
4.264.451208810010.133
4.094.261262310010.167
3.944.091309010010.221
3.813.941355210010.285
3.693.811399210010.376
3.583.691441310010.526
3.483.581486110010.729
3.393.481524710010.939
3.33.391562010011.174
ReflectionResolution: 3.3→50 Å / Num. all: 213602 / Num. obs: 213602 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 104.363 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.3-3.390.0122.02178392156201100
3.39-3.480.0122.62176841152471100
3.48-3.580.0123.36165923148611100
3.58-3.690.0124.68169268144131100
3.69-3.810.0126.49162400139921100
3.81-3.940.0128.41150652135521100
3.94-4.090.01210.84152802130901100
4.09-4.260.01213.95145282126231100
4.26-4.450.01217.34136093120881100
4.45-4.670.01221.73134360115971100
4.67-4.920.01224.54122061110201100
4.92-5.220.01228.82119686104691100
5.22-5.580.01231.5610925598361100
5.58-6.020.01234.8110441692091100
6.02-6.60.01236.529379184661100
6.6-7.380.01242.128513476941100
7.38-8.520.01246.247273968291100
8.52-10.440.01249.936161858471100
10.44-14.760.01254.054728945821100
14.76-500.01254.5249252567196.5

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_978refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
XDSdata reduction
PHENIXdev_978phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.3→49.484 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8899 / SU ML: 0.33 / σ(F): 1.99 / Phase error: 17.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 10749 5.03 %FROM PDB ENTRY 2VQE
Rwork0.1534 ---
obs0.1554 213574 99.97 %-
all-213574 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.15 Å2 / ksol: 0.262 e/Å3
Displacement parametersBiso max: 550 Å2 / Biso mean: 120.8243 Å2 / Biso min: 26.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.4527 Å20 Å20 Å2
2--2.4527 Å20 Å2
3---10.6777 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19127 33097 418 907 53549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00657427
X-RAY DIFFRACTIONf_angle_d0.94685762
X-RAY DIFFRACTIONf_chiral_restr0.06510541
X-RAY DIFFRACTIONf_plane_restr0.0054924
X-RAY DIFFRACTIONf_dihedral_angle_d17.61626342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3-3.33740.31353420.258666186960
3.3374-3.37670.26073840.239367177101
3.3767-3.41780.28473520.228966707022
3.4178-3.46110.2483390.215967127051
3.4611-3.50660.24593660.21266977063
3.5066-3.55470.25373520.208766987050
3.5547-3.60540.25053610.203466677028
3.6054-3.65920.25423830.186767097092
3.6592-3.71640.21083500.171967007050
3.7164-3.77730.19893610.163667047065
3.7773-3.84240.19443840.157666787062
3.8424-3.91220.19473560.15767097065
3.9122-3.98750.18753400.151967647104
3.9875-4.06880.19173440.147867317075
4.0688-4.15720.20893450.143667277072
4.1572-4.25390.18513590.1467357094
4.2539-4.36020.18433510.136267187069
4.3602-4.4780.17443700.131367707140
4.478-4.60970.18283160.128367777093
4.6097-4.75840.17263520.127867277079
4.7584-4.92830.17383320.120167937125
4.9283-5.12540.15933410.123267857126
5.1254-5.35840.17123820.132267497131
5.3584-5.64060.16863420.125468127154
5.6406-5.99340.1623900.122367857175
5.9934-6.45520.18143440.127768397183
6.4552-7.10320.1643470.124968647211
7.1032-8.12710.15693700.126468667236
8.1271-10.22440.18693990.154169337332
10.2244-49.48920.21683950.206271717566
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43770.136-0.16050.5838-0.11270.5273-0.003-0.032-0.05050.16320.08680.17250.1630.0792-0.07820.5770.1530.06340.5768-0.03260.817143.70683.4459-12.1861
21.9945-0.31570.2790.4806-0.08860.3594-0.0296-0.99510.46190.29030.0973-0.1681-0.15580.0818-0.06840.8338-0.16690.04981.6391-0.60861.1678222.8545129.25899.8616
31.70670.698-0.63720.41-0.510.2852-0.2608-0.1499-0.6323-0.25540.1627-0.5140.27970.19960.09070.92260.18380.05120.9094-0.09651.0837163.470169.0326-25.1122
42.76441.29491.39332.9191-2.26084.37080.391-0.07183.12410.5747-0.5708-1.0079-1.1022-0.17320.08581.828-0.24590.22961.4785-0.04751.7125181.227132.097-40.4929
55.63960.37462.49374.5804-4.04526.047-0.37890.42661.14740.02990.3719-0.3101-0.96060.2613-0.01792.0253-0.10710.53470.7363-0.04681.2722157.3934156.9003-35.9141
64.11940.61143.4496.00481.97675.66160.1868-0.00871.228-0.8061-0.34790.7739-0.8712-1.02340.13631.30010.06210.39960.82550.0771.8603150.8497155.9118-27.1545
76.32120.3767-0.32215.2711-2.30296.62530.26160.66041.4239-0.7493-0.1864-0.6346-1.39611.7577-0.07991.105-0.33430.59291.1694-0.08451.5776167.4805162.1616-18.7011
83.32992.11960.46513.9921-2.29624.11180.5119-0.75411.09730.3862-0.0534-0.2525-0.79380.9169-0.41630.7522-0.28480.44561.0559-0.58661.5295174.5213156.8813-6.4097
94.47681.1020.61155.8707-0.92081.6146-0.12960.45421.03841.47441.061-1.5796-0.51522.0192-0.84461.6212-0.4660.02232.0787-0.77522.2374190.7094161.5066-3.9051
102.9047-0.47021.84184.89-0.94893.4610.05510.16040.2043-0.77770.3052-0.3971-0.69880.391-0.33121.1844-0.12080.62780.7632-0.25671.6557160.6985156.0966-18.1448
111.32721.61460.59967.1634-1.93091.637-0.1685-0.05340.18990.40850.01570.3048-0.3845-0.0640.13342.3328-0.20440.32030.6306-0.00442.505163.9368174.221-22.928
120.1152-0.28720.16120.8597-0.39140.2328-0.0133-0.8180.25110.57280.15910.1843-0.3462-0.2673-0.03571.330.01290.06972.7507-1.00721.268205.2787140.988534.2517
131.0912-1.8749-0.16443.24980.22611.671-0.1514-1.30620.1830.43090.20490.63020.1481-0.73120.04960.9256-0.09680.21092.633-0.74711.2992190.3185132.506418.3293
147.1832-7.1602-3.00627.25423.13024.04230.2413-1.01110.32520.62140.50130.1709-0.81370.4925-0.74831.667-0.31530.13131.2557-0.17541.1184153.9536111.284838.067
156.48880.08631.12953.6925-0.77082.53350.1083-1.35110.86590.7503-0.1333-0.3991-0.72070.7640.04651.1179-0.04920.0940.9856-0.25660.7152160.3059112.974225.7591
162.3731.09291.15963.0572-3.6227.33860.3186-0.18470.23960.6082-0.15430.25510.313-0.1719-0.15411.20540.14420.38450.6611-0.09770.94136.0301103.939431.2148
174.1413-1.89811.6163.350.85794.04480.2632-1.80170.57171.92620.16770.5248-0.7111-0.4418-0.39892.14780.02160.49771.331-0.23711.0067132.3233110.344647.6953
186.48790.4893-5.68575.1509-0.36514.97441.39410.03551.7780.1429-0.0442-0.0119-1.679-0.1593-1.3560.89660.11040.12230.57430.0390.841139.6965114.149323.52
196.0282-6.236-6.00796.44646.17856.4704-0.6498-1.79281.36611.47890.43870.0651-0.15760.16830.1270.8977-0.02530.07451.5486-0.62261.3179162.1133126.428.5214
204.8661-1.7638-4.93084.16772.0765.021-0.1691-0.28820.13940.4454-0.10350.0014-0.1250.29780.24440.8102-0.19250.14771.8302-0.56741.041184.1399121.568-2.0195
214.8080.3073-2.88824.9676-1.56346.23730.3729-0.5031.30410.55950.6786-0.3239-0.05040.6613-0.99650.739-0.2370.19680.9721-0.55191.0573162.0523129.09985.0333
227.0075-5.0955.45156.8046-2.56796.2987-0.6218-0.21492.05471.09680.6699-0.7714-1.25891.06980.01551.074-0.27850.16730.9026-0.50031.6018167.9398132.98935.7353
237.82866.066-2.78828.1917-2.1811.87470.6547-1.00062.65021.0978-0.38441.4528-0.4466-0.6184-0.2870.63940.02340.18770.876-0.2671.1929145.4855129.10120.8883
243.01131.3693-2.97318.3681-0.46323.0386-0.54782.967-1.6361-0.6437-0.18451.5651.401-1.9660.67580.5692-0.0950.021.1482-0.21011.0847152.7424119.8695-10.3996
257.54992.896-4.58584.9418-3.74577.7022-0.10190.07870.31450.39070.2338-0.0146-0.0522-0.6512-0.12950.50750.07520.14730.5319-0.26991.0713145.6554116.56731.3301
262.02710.65692.12472.03150.95254.0024-0.1694-0.63740.30040.3480.10160.33770.060.7530.04990.559-0.06980.21310.7326-0.24190.7979153.3903120.4586-0.0427
279.7806-5.50445.58213.098-3.14273.1907-0.4278-0.78761.46010.4148-0.07660.4948-1.3979-1.45850.46660.89960.1850.27330.9029-0.22541.3176136.6359133.6256-8.9581
282.32250.3639-3.47323.91760.93715.7565-0.03371.6679-0.0612-1.38350.10250.17530.1793-0.1183-0.0451.15180.1328-0.09482.33530.01590.665174.1655114.784-93.1846
298.60262.07412.54834.70620.09244.81380.08621.7104-0.1551-0.92820.0314-0.2842-0.31690.072-0.1190.98960.15510.20891.36150.04810.7442175.0837115.6123-86.8059
306.87745.55325.08714.58294.15133.7808-1.01610.30432.4282-1.4701-0.08332.031-1.7999-0.45011.05211.36540.2650.04571.34280.4551.7977165.7581131.4971-73.5266
313.70222.77821.86082.23941.08531.5746-0.1352-0.43192.98540.3186-0.3131.1598-1.33990.4090.40181.1172-0.29430.06971.3203-0.64722.3011217.6421143.0997-22.6294
326.53346.09790.1086.26210.30950.2219-0.3210.63590.6281-0.5270.1132-0.2081-0.09210.11320.18461.3613-0.16220.53461.08790.38473.1509239.2366153.1206-24.4864
338.77042.8842-3.01465.5542-2.94518.7749-0.23070.50971.12150.1040.009-0.6523-0.6711.41940.19960.7417-0.14820.20411.0882-0.14211.7862245.0379143.7627-22.5039
347.9273.6561-2.52996.7446-0.88443.01780.1178-0.08461.05230.1441-0.14960.5519-0.3394-0.14210.01921.4248-0.82780.46841.7907-0.18582.7077253.4786147.6885-36.5125
359.16497.68545.52579.52884.13276.7095-0.54461.00320.2354-0.45310.1134-0.0081-0.36-0.31660.35350.96060.28030.29641.60720.15831.1741233.2176137.4235-37.1623
366.32645.930.57795.69850.57045.55660.1485-0.3411-0.337-0.28750.74731.22230.9426-0.208-0.83871.09510.1563-0.19792.04190.45871.5965219.5769125.5777-38.6411
371.5603-1.6821-1.47413.69080.88321.66160.0290.01381.01420.00050.0504-0.283-0.38030.0077-0.08440.7712-0.31980.17071.1877-0.06811.6761235.0239136.4296-30.5134
384.3753-3.19994.8095.494-2.02156.15760.18811.0920.9935-0.73520.0647-1.0955-0.022.0785-0.20320.7552-0.13290.4661.3826-0.15481.5174250.5843135.2934-30.2891
396.9245-0.20553.7043.25632.21913.6581-0.48691.9678-0.3801-0.93650.3161-0.89960.28510.63850.12721.2658-0.15720.15911.85850.04231.4598237.7046129.4278-40.1899
409.29691.14876.56652.14120.43164.71450.3822-0.00061.49740.7898-0.34431.7959-1.1579-1.5786-0.05761.39530.63710.42371.8624-0.01631.8946219.3847125.8877-44.6485
416.87321.0127-0.18947.7444-0.44221.71150.52610.00660.57540.03290.25930.1396-0.14610.4729-0.74490.47020.16090.25370.6553-0.060.8269140.1512122.7088-30.3506
429.3928.52377.60927.76586.92926.18270.127-0.12511.3405-0.2367-0.13830.5564-0.6882-0.25760.05220.65960.16960.27180.718-0.03121.075139.3723132.308-31.4762
432.70822.75512.56576.9625.50755.46040.0497-0.27920.7053-0.1937-0.58461.672-0.9419-2.21280.53980.48790.18930.15240.79690.1971.3226126.6872125.8637-27.324
443.7253-1.434-1.7553.71913.61163.54960.03750.29380.45520.05220.18741.0532-1.3966-0.887-0.22341.00020.10660.15890.7310.22231.53130.6184133.0958-29.7149
455.64471.43625.13253.66552.65646.0695-0.03310.29641.0115-0.80520.21910.1663-1.12770.2257-0.21020.80490.08060.17950.55130.14071.2505133.5959131.8698-38.4318
469.53460.76675.31144.2706-0.58027.38040.15-0.43251.13520.74280.6410.1703-0.4435-0.1112-0.75960.79140.02630.31520.6687-0.06271.3135145.7397140.0393-16.7243
477.85337.02876.2016.39785.93876.28350.44490.08280.05190.3749-0.1142-0.6689-0.00120.1397-0.30340.48290.10780.19360.49480.10121.0915143.4364129.3158-18.4462
481.29352.2552-1.06924.4349-3.52039.9158-0.21990.0175-0.0370.03730.0842-0.40440.85410.71120.09040.58250.1190.09170.55040.03181.088133.8873108.8729-24.2379
498.1476-3.87777.25512.5345-2.4267.9928-0.5666-0.6806-2.12880.93190.67160.45522.10321.2384-0.09960.93290.35370.42710.80260.18531.6877125.5825109.7467-12.0318
502.7274.38451.60427.48761.98942.02530.9486-0.7769-0.11281.1052-0.7287-0.55461.258-1.5472-0.19920.8215-0.15140.04941.31520.10161.0967134.1892119.3597-8.6969
516.97235.46926.67457.45556.83188.11330.09560.19550.04340.33940.0939-0.0351-0.0008-0.1034-0.20430.64240.26110.26330.71760.05851.0645126.3187118.872-18.8087
527.57083.1216-1.16584.6918-3.51272.87980.0544-0.76381.61320.475-0.057-0.2123-1.0488-0.3126-0.02340.75530.15920.3140.7160.02531.7081122.5005119.9066-15.4552
532.7172.0746-1.58329.01742.63334.38090.23880.0147-0.6860.04840.1637-0.00170.27560.3502-0.40770.55380.15350.16440.42390.12790.8912131.2681117.2473-18.8115
541.281.05181.00679.39452.07012.13730.1707-0.14071.02140.0345-0.12170.4996-0.87370.3546-0.00271.3081-0.38060.16611.4645-0.90593.0068238.9768167.1648-3.7997
558.32023.48546.18692.52253.00545.32690.09580.0996-0.5480.2479-0.0518-1.1126-0.35630.9754-0.06461.3129-0.4943-0.24541.7878-0.83782.7715249.2774162.4376-3.1801
562.56593.0238-0.14053.99230.41872.7612-0.31640.15340.7074-0.1397-0.3995-0.1-0.76651.06630.66771.1215-0.63220.10651.7438-0.4362.5743244.4611159.2299-12.7041
571.8869-1.30720.91682.8004-0.0182.49970.26430.28950.75510.6454-0.0811-0.1802-0.92980.7335-0.15161.4212-0.4560.1611.2013-0.55793.1942239.1973165.1951-7.5923
580.4036-1.3351-1.40786.8877.81359.04380.1639-0.65312.2220.34870.09350.3275-1.65710.5816-0.24661.9763-0.0368-0.01850.9822-0.32142.5826229.1709172.7722-15.8952
591.0884-0.67460.4674.6279-1.93093.38810.192-0.68681.25140.4966-0.2793-0.5419-0.84960.38120.07921.0981-0.36380.20041.4513-0.58651.8549225.8613147.6491-5.7234
606.2436-3.71862.67372.4481-2.79137.61840.4676-0.0993-0.4594-1.0984-0.19210.87761.5043-0.783-0.2471.0719-0.33570.06781.7815-0.84251.227222.6523124.7233-6.8484
613.24211.59872.68360.79261.3722.55070.4333-0.46110.71160.9942-0.76030.4405-0.6461-0.23510.37991.6075-0.2359-0.11032.39-1.38282.7354221.2991162.153527.859
621.6106-3.4725-2.88077.97295.57545.97270.1061-0.49271.20651.17630.14-0.377-2.40420.2134-0.28972.5562-0.0263-0.11632.1678-1.48422.7055227.2583165.957123.686
635.78471.20083.88592.16780.96727.36230.2928-0.88870.46541.5508-0.3694-0.8284-0.5290.57390.04171.3708-0.26520.12222.4305-0.93911.4388225.2745142.07617.9352
642.8730.51371.0941.0258-0.84041.5711-0.2805-0.6090.96190.2510.2356-0.0881-0.36610.28820.03871.0914-0.24860.20622.0959-0.80521.2901218.3892135.306913.6759
652.6307-0.67211.11558.1286-1.14551.17370.4496-1.36130.86212.4352-1.0420.9848-1.1049-0.61140.6622.2816-0.2151-0.29582.4599-1.59833.1331230.0343169.436531.7503
664.5694-5.7227-3.12987.37642.84997.58980.039-0.89251.34980.3940.16040.7624-1.46510.3907-0.23972.49630.28980.63752.338-1.14422.2997222.8514171.146240.391
675.8546-5.2475-4.98684.83924.55514.30130.4931-0.90471.18461.40370.2717-2.0655-1.53172.9408-0.78331.6421-0.3090.1763.0468-0.77272.3026215.5683157.760336.2131
687.4138-5.1566-1.18944.4674-2.02429.42220.6947-0.34930.52161.4611-0.2165-1.4672-0.74391.8947-0.52561.96050.0713-0.52062.8116-1.16161.8335227.4678156.256634.062
698.7672-1.93986.21299.7972-2.84425.1782-0.49520.5312-0.0967-0.30180.4786-0.3531-0.3017-0.25220.04290.4627-0.01090.17230.7699-0.11670.8886213.158118.5943-69.2536
707.0803-0.50121.69874.4442-0.60356.5885-0.08060.11960.3055-0.166-0.0364-0.8156-0.01391.86460.11790.6968-0.12270.22421.1738-0.01740.925217.3025114.8981-62.5371
714.13433.6267-5.06746.6818-4.23886.21820.0647-0.05990.4261-0.2029-0.0375-1.1642-0.19561.57-0.04740.5583-0.02890.09771.1677-0.10591.0113221.2417121.9611-64.3926
724.67861.61695.50822.0790.46787.8849-0.4038-0.6370.540.0908-0.45940.3531-0.2762-0.62290.80190.71920.00770.23340.9266-0.17361.0843211.3838125.8974-64.7432
733.0675-0.62512.90278.61995.23886.7477-0.21050.67271.2068-0.696-0.5582-1.2027-1.05911.29470.76260.8985-0.14470.17730.94370.29331.1029211.0102129.728-69.7464
740.94780.25520.83846.2851-4.48334.33330.23810.51530.05290.279-0.0455-0.0772-0.28230.4179-0.21081.0379-0.0560.45571.2932-0.33361.19193.7347110.2081-57.5097
752.6332-1.63163.75351.0002-2.32515.32840.3836-0.0651-0.2535-0.15430.36470.08060.74110.4429-0.72350.69540.316-0.04791.02060.13451.2097153.299189.0035-13.2323
764.40920.4821-2.30033.93991.14731.7781-0.1899-0.0983-0.38810.40720.2668-0.65140.56360.8844-0.05680.68610.3042-0.18621.01910.04730.9378173.876579.03510.8826
775.0471-3.55652.1913.0755-0.32614.3827-0.1391-0.1453-2.0029-0.46870.05360.92420.76370.67780.00280.8852-0.07380.22931.7577-0.48362.4096274.0032116.6762-8.1766
784.4448-6.21343.97748.6958-5.42795.2279-0.00470.34840.8674-0.13190.32431.0413-0.061-0.1355-0.30510.64030.3114-0.191.5782-0.36161.7655268.8301120.9716-5.159
796.74143.8725-0.25924.4577-3.1414.2038-0.0416-0.46510.63450.1097-0.8865-0.8308-0.10330.92260.91240.7102-0.00190.09421.9227-0.50531.9243275.9917122.7674-0.9486
808.7637.6596-2.35329.2325-2.65282.17440.5067-1.9933-0.57961.1615-0.8911-1.4084-0.48571.13220.3840.9269-0.0638-0.16231.8345-0.06131.0821265.5499105.08918.9516
812.6228-3.12431.1079.1743-3.77114.9456-0.0546-0.994-0.29560.7296-0.2478-0.3540.20540.51760.26590.9416-0.04530.04632.4293-0.2461.2341249.984999.278313.906
824.11743.44853.59764.06541.17686.0987-0.3132-0.1019-1.06440.04630.40870.33820.13540.9969-0.08920.69730.08820.04221.5432-0.15841.275240.988103.81912.4567
838.1201-2.4107-2.20634.3693-3.89557.22230.4196-0.98240.13110.8958-0.4241-0.2079-0.0688-0.56080.00521.0171-0.4938-0.07072.8148-0.60351.3709220.5487117.239834.3622
843.45190.0061-2.0595.01094.73075.7327-0.7551-3.1422.13932.09881.8917-0.76960.05652.0375-1.13061.3562-0.14980.03012.821-0.68781.9898232.1104118.889139.7495
850.26150.985-0.10393.7787-0.26720.27520.309-0.9323-0.02330.3783-0.0986-0.0125-0.31260.3436-0.22051.0027-0.20410.13662.5448-0.52971.4048228.4715121.226730.7577
861.63633.41322.96217.11796.17835.36220.1611-0.1203-0.00081.0650.2048-0.98260.92621.1161-0.38610.98510.1539-0.34252.3539-0.50751.1169215.7497124.65427.0206
872.2269-0.0372-0.74812.1068-0.70823.9812-0.0863-1.05610.98580.3263-0.36610.16180.3878-0.12680.37770.95330.1211-0.04412.2609-0.86621.2914216.7172134.312320.522
885.65255.2816-4.48444.9384-4.18043.604-0.58794.37121.7576-2.47430.68360.5692-0.5751-0.6439-0.13511.16590.1515-0.04941.79470.35591.0007141.4082110.7414-73.9276
897.6647-4.8858-0.63053.18650.82228.33610.45821.2144-0.5511-0.6545-0.01150.5406-0.5031-0.2568-0.39920.6560.0698-0.1490.7555-0.01131.0218145.0101104.3475-66.3479
909.4051-1.85321.18423.0816-0.29231.71230.2687-1.3592-0.14060.19750.2345-0.01490.18810.6738-0.49870.61820.0093-0.12921.1725-0.11790.7236143.7808101.902-56.2219
915.0463-0.0192-4.39575.57570.54623.87940.00291.3291-2.2223-0.0861-0.07871.03731.0528-1.28460.0910.8013-0.1499-0.31291.39370.19191.8417131.333297.7799-63.6279
928.1444-0.26643.55950.8768-0.87053.01560.0239-0.7240.27430.3680.35610.2512-0.1716-0.1293-0.35871.03520.10970.52730.69510.03281.3152117.490676.974715.4409
932.321-0.40040.53670.3874-1.17565.1293-0.1291-0.23690.87140.39410.2810.71160.0135-0.0385-0.16620.83360.04220.30050.6015-0.02951.5828115.042477.321610.9058
945.30074.32925.58283.57934.38766.5644-0.7547-0.60292.2533-0.4833-0.23820.8198-2.6976-0.75430.99781.36180.20460.53470.6746-0.01841.7399109.707786.511320.9646
955.47810.8464-0.37961.7145-3.68868.9219-0.0632-0.15390.5508-0.3947-0.073-0.1225-0.6855-0.13860.10811.01520.3010.33580.73270.36772.0417100.99279.39595.8698
966.34283.66655.45095.75412.18318.91320.3116-1.0263-0.07530.6808-0.11640.9039-0.1957-0.7858-0.20151.1797-0.0640.79150.69610.16671.8502101.245175.145716.7365
972.1880.72281.25022.91833.01313.2451-0.19090.94360.4156-0.73240.2258-0.41710.02310.0335-0.02940.8153-0.01730.19830.91370.28380.7754120.284280.8273-38.1483
981.58550.2776-0.1462.98490.43972.9968-0.15830.09180.2074-0.5880.24690.74110.1318-0.3886-0.07370.6723-0.0937-0.10180.78610.20981.2075122.216184.6572-35.269
994.5206-4.0555-0.04454.1049-1.62025.9283-0.3802-0.05850.4832-0.19640.3836-0.41510.16220.00410.00590.7277-0.1377-0.00391.04220.03361.2302138.248485.7121-44.089
1006.0068-3.6368-4.8787.17011.17934.5942-0.1064-1.7644.97570.3552-0.4576-0.7135-2.6080.57120.59321.5994-0.15120.26790.7956-0.26662.0192181.0438139.8207-63.7158
1016.17183.80982.03133.52162.65532.4268-0.60520.40121.6516-0.434-0.03310.444-0.959-0.30210.62251.98180.13640.25491.18530.09691.8232175.1267140.8427-71.9223
1023.4652-2.0571-3.12235.5653.74833.639-0.06651.14310.984-0.6773-0.29950.7775-0.9275-1.02670.30941.01440.57630.07531.72250.33551.0434172.8204129.0468-76.5567
1039.17454.72196.72258.06713.63236.50240.39591.72841.8033-1.57880.2075-1.5113-1.36431.3096-0.62070.9730.35160.57721.00490.39981.4503181.6267132.9247-74.1737
1046.2379-4.929-5.84463.92744.71155.74150.2399-0.42360.5135-0.08680.3518-2.8113-0.30183.1336-0.59430.66360.0877-0.00031.40210.03661.2167186.8392128.2925-65.6991
1057.4646-2.2716-3.58997.34852.1814.22730.56310.04630.7096-0.14310.45820.2321-0.7011-0.0836-0.980.81490.0420.20661.10120.22370.6373176.0724126.953-66.8099
1062.94851.5972.5672.50670.34382.90.29940.31860.350.12290.1271-1.20320.22920.7454-0.40280.8030.50470.13541.52450.18241.2499193.2369125.7966-70.6526
1076.65980.7389-3.37615.2581-4.3114.7269-0.15641.0325-1.4162-1.39120.55790.57712.1298-2.219-0.38481.3459-0.2264-0.61362.0866-0.45181.9322252.4158113.332727.7244
1082.3121.94190.41711.63280.25253.7578-0.5918-1.6972-0.15781.58750.4689-0.3031-0.3286-1.03820.10721.93670.6871-0.54843.34520.2131.5365251.987999.767742.2742
1097.38976.9809-6.40767.9186-4.29397.8957-0.5656-0.96080.23211.31920.1463-1.9171-0.02831.13350.41491.3975-0.2006-0.11662.4516-0.14251.6258247.036793.225137.2863
1100.19170.63960.14512.13340.48430.1099-0.2483-1.31560.57621.03580.0439-0.5631-0.31610.03310.23251.14130.0073-0.22613.2399-0.1890.9068247.8059105.005129.5588
1115.65241.62752.11515.0383-0.1662.92220.3907-1.2626-0.8070.69240.2268-0.95480.24331.0418-0.59741.1176-0.0025-0.182.2410.01241.2069250.716296.788829.1057
1124.4295-1.48265.20362.1509-1.31456.2206-0.4922-0.2588-0.07470.58340.3275-0.8028-0.46451.42570.14071.3809-0.2176-0.13011.58160.05291.464242.20997.391718.0642
1132.9133-0.34123.62251.9271-0.43897.35780.3621-0.0764-0.2989-0.150.20920.49831.0225-0.167-0.60871.031-0.1080.09790.57150.16071.0469108.084241.8881-19.6453
1140.0297-0.0097-0.01460.00850.0190.04780.24-0.654-0.0040.8430.20041.0837-0.0388-0.3291-0.43950.9828-0.08780.04341.04070.40821.2924105.664851.4786-14.7462
1151.94012.54581.84555.07153.2964.0736-0.26160.80580.4156-0.48790.4881-0.1505-1.53571.06-0.23371.2568-0.5101-0.01071.09960.52731.6307103.345152.1199-31.225
1165.0823-5.9474-4.77239.67733.73975.7341-0.03150.747-0.908-0.4243-0.72141.67171.2822-2.24590.6491.2744-0.4459-0.25451.54120.09751.310592.939347.7888-38.8206
1177.9137-3.0295-1.11951.6840.9591.2554-0.3357-0.88280.87131.41820.0969-0.2884-0.80960.74750.24551.2067-0.2322-0.0181.9355-0.94241.7934251.952125.04572.8101
1188.8742-7.29495.74358.9395-1.27488.28140.03680.0070.4296-0.83180.0849-1.1456-0.09480.8954-0.10920.8951-0.09170.27791.3455-0.78681.8168248.3542129.94094.3806
1198.55721.95591.22062.2694-1.13348.23550.0402-1.00360.88870.6972-0.59190.0781-0.8601-0.03860.51761.0068-0.1508-0.17522.525-1.09731.7869254.1537133.397210.7119
1203.44524.29992.8738.5937-0.24677.08160.502-0.95720.8287-0.04090.4027-0.8073-0.18721.032-0.86571.55920.5258-0.11863.0311-0.55422.4391193.573799.1599-0.7262
1214.12182.8028-0.91053.2053-2.56273.11360.1116-1.0494-0.00290.55110.2375-3.57050.80062.8714-0.33721.52850.6201-0.32633.3882-0.57133.264203.435694.59635.2126
1228.20320.40891.13146.6943-5.2644.39650.3483-1.20783.25912.50221.1655-0.3314-2.09931.5171-1.5882.2643-0.24650.45962.2147-0.56412.3257184.2864126.2336-39.0763
1231.99991.43395.19391.9998-0.34072.60081.13162.5074-1.3305-1.6725-1.317-3.33351.58442.70780.18641.03950.7697-0.15391.7191-0.13941.7447203.4825102.2805-19.7687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:920)A5 - 920
2X-RAY DIFFRACTION2chain 'A' and (resseq 921:1400)A921 - 1400
3X-RAY DIFFRACTION3chain 'A' and (resseq 1401:1532)A1401 - 1532
4X-RAY DIFFRACTION4chain 'A' and (resseq 1533:1541)A1533 - 1541
5X-RAY DIFFRACTION5chain 'B' and (resseq 7:25)B7 - 25
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:64)B26 - 64
7X-RAY DIFFRACTION7chain 'B' and (resseq 65:86)B65 - 86
8X-RAY DIFFRACTION8chain 'B' and (resseq 87:122)B87 - 122
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:148)B123 - 148
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:226)B149 - 226
11X-RAY DIFFRACTION11chain 'B' and (resseq 227:240)B227 - 240
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:112)C2 - 112
13X-RAY DIFFRACTION13chain 'C' and (resseq 113:207)C113 - 207
14X-RAY DIFFRACTION14chain 'D' and (resseq 2:34)D2 - 34
15X-RAY DIFFRACTION15chain 'D' and (resseq 35:67)D35 - 67
16X-RAY DIFFRACTION16chain 'D' and (resseq 68:148)D68 - 148
17X-RAY DIFFRACTION17chain 'D' and (resseq 149:181)D149 - 181
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)D182 - 209
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:14)E5 - 14
20X-RAY DIFFRACTION20chain 'E' and (resseq 15:27)E15 - 27
21X-RAY DIFFRACTION21chain 'E' and (resseq 28:50)E28 - 50
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:63)E51 - 63
23X-RAY DIFFRACTION23chain 'E' and (resseq 64:79)E64 - 79
24X-RAY DIFFRACTION24chain 'E' and (resseq 80:86)E80 - 86
25X-RAY DIFFRACTION25chain 'E' and (resseq 87:103)E87 - 103
26X-RAY DIFFRACTION26chain 'E' and (resseq 104:140)E104 - 140
27X-RAY DIFFRACTION27chain 'E' and (resseq 141:154)E141 - 154
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:32)F1 - 32
29X-RAY DIFFRACTION29chain 'F' and (resseq 33:92)F33 - 92
30X-RAY DIFFRACTION30chain 'F' and (resseq 93:101)F93 - 101
31X-RAY DIFFRACTION31chain 'G' and (resseq 2:11)G2 - 11
32X-RAY DIFFRACTION32chain 'G' and (resseq 12:20)G12 - 20
33X-RAY DIFFRACTION33chain 'G' and (resseq 21:52)G21 - 52
34X-RAY DIFFRACTION34chain 'G' and (resseq 53:57)G53 - 57
35X-RAY DIFFRACTION35chain 'G' and (resseq 58:79)G58 - 79
36X-RAY DIFFRACTION36chain 'G' and (resseq 80:92)G80 - 92
37X-RAY DIFFRACTION37chain 'G' and (resseq 93:109)G93 - 109
38X-RAY DIFFRACTION38chain 'G' and (resseq 110:129)G110 - 129
39X-RAY DIFFRACTION39chain 'G' and (resseq 130:144)G130 - 144
40X-RAY DIFFRACTION40chain 'G' and (resseq 145:156)G145 - 156
41X-RAY DIFFRACTION41chain 'H' and (resseq 1:18)H1 - 18
42X-RAY DIFFRACTION42chain 'H' and (resseq 19:29)H19 - 29
43X-RAY DIFFRACTION43chain 'H' and (resseq 30:41)H30 - 41
44X-RAY DIFFRACTION44chain 'H' and (resseq 42:53)H42 - 53
45X-RAY DIFFRACTION45chain 'H' and (resseq 54:62)H54 - 62
46X-RAY DIFFRACTION46chain 'H' and (resseq 63:72)H63 - 72
47X-RAY DIFFRACTION47chain 'H' and (resseq 73:85)H73 - 85
48X-RAY DIFFRACTION48chain 'H' and (resseq 86:95)H86 - 95
49X-RAY DIFFRACTION49chain 'H' and (resseq 96:100)H96 - 100
50X-RAY DIFFRACTION50chain 'H' and (resseq 101:106)H101 - 106
51X-RAY DIFFRACTION51chain 'H' and (resseq 107:116)H107 - 116
52X-RAY DIFFRACTION52chain 'H' and (resseq 117:127)H117 - 127
53X-RAY DIFFRACTION53chain 'H' and (resseq 128:138)H128 - 138
54X-RAY DIFFRACTION54chain 'I' and (resseq 2:25)I2 - 25
55X-RAY DIFFRACTION55chain 'I' and (resseq 26:32)I26 - 32
56X-RAY DIFFRACTION56chain 'I' and (resseq 33:53)I33 - 53
57X-RAY DIFFRACTION57chain 'I' and (resseq 54:88)I54 - 88
58X-RAY DIFFRACTION58chain 'I' and (resseq 89:97)I89 - 97
59X-RAY DIFFRACTION59chain 'I' and (resseq 98:117)I98 - 117
60X-RAY DIFFRACTION60chain 'I' and (resseq 118:128)I118 - 128
61X-RAY DIFFRACTION61chain 'J' and (resseq 3:29)J3 - 29
62X-RAY DIFFRACTION62chain 'J' and (resseq 30:42)J30 - 42
63X-RAY DIFFRACTION63chain 'J' and (resseq 43:47)J43 - 47
64X-RAY DIFFRACTION64chain 'J' and (resseq 48:70)J48 - 70
65X-RAY DIFFRACTION65chain 'J' and (resseq 71:78)J71 - 78
66X-RAY DIFFRACTION66chain 'J' and (resseq 79:85)J79 - 85
67X-RAY DIFFRACTION67chain 'J' and (resseq 86:93)J86 - 93
68X-RAY DIFFRACTION68chain 'J' and (resseq 94:100)J94 - 100
69X-RAY DIFFRACTION69chain 'K' and (resseq 11:34)K11 - 34
70X-RAY DIFFRACTION70chain 'K' and (resseq 35:57)K35 - 57
71X-RAY DIFFRACTION71chain 'K' and (resseq 58:75)K58 - 75
72X-RAY DIFFRACTION72chain 'K' and (resseq 76:100)K76 - 100
73X-RAY DIFFRACTION73chain 'K' and (resseq 101:110)K101 - 110
74X-RAY DIFFRACTION74chain 'K' and (resseq 111:126)K111 - 126
75X-RAY DIFFRACTION75chain 'L' and (resseq 5:32)L5 - 32
76X-RAY DIFFRACTION76chain 'L' and (resseq 33:128)L33 - 128
77X-RAY DIFFRACTION77chain 'M' and (resseq 2:14)M2 - 14
78X-RAY DIFFRACTION78chain 'M' and (resseq 15:21)M15 - 21
79X-RAY DIFFRACTION79chain 'M' and (resseq 22:61)M22 - 61
80X-RAY DIFFRACTION80chain 'M' and (resseq 62:83)M62 - 83
81X-RAY DIFFRACTION81chain 'M' and (resseq 84:93)M84 - 93
82X-RAY DIFFRACTION82chain 'M' and (resseq 94:119)M94 - 119
83X-RAY DIFFRACTION83chain 'N' and (resseq 2:11)N2 - 11
84X-RAY DIFFRACTION84chain 'N' and (resseq 12:16)N12 - 16
85X-RAY DIFFRACTION85chain 'N' and (resseq 17:24)N17 - 24
86X-RAY DIFFRACTION86chain 'N' and (resseq 25:29)N25 - 29
87X-RAY DIFFRACTION87chain 'N' and (resseq 30:61)N30 - 61
88X-RAY DIFFRACTION88chain 'O' and (resseq 2:15)O2 - 15
89X-RAY DIFFRACTION89chain 'O' and (resseq 16:49)O16 - 49
90X-RAY DIFFRACTION90chain 'O' and (resseq 50:73)O50 - 73
91X-RAY DIFFRACTION91chain 'O' and (resseq 74:88)O74 - 88
92X-RAY DIFFRACTION92chain 'P' and (resseq 1:19)P1 - 19
93X-RAY DIFFRACTION93chain 'P' and (resseq 20:43)P20 - 43
94X-RAY DIFFRACTION94chain 'P' and (resseq 44:52)P44 - 52
95X-RAY DIFFRACTION95chain 'P' and (resseq 53:62)P53 - 62
96X-RAY DIFFRACTION96chain 'P' and (resseq 63:83)P63 - 83
97X-RAY DIFFRACTION97chain 'Q' and (resseq 2:17)Q2 - 17
98X-RAY DIFFRACTION98chain 'Q' and (resseq 18:82)Q18 - 82
99X-RAY DIFFRACTION99chain 'Q' and (resseq 83:100)Q83 - 100
100X-RAY DIFFRACTION100chain 'R' and (resseq 19:23)R19 - 23
101X-RAY DIFFRACTION101chain 'R' and (resseq 24:28)R24 - 28
102X-RAY DIFFRACTION102chain 'R' and (resseq 29:36)R29 - 36
103X-RAY DIFFRACTION103chain 'R' and (resseq 37:43)R37 - 43
104X-RAY DIFFRACTION104chain 'R' and (resseq 44:52)R44 - 52
105X-RAY DIFFRACTION105chain 'R' and (resseq 53:76)R53 - 76
106X-RAY DIFFRACTION106chain 'R' and (resseq 77:88)R77 - 88
107X-RAY DIFFRACTION107chain 'S' and (resseq 2:12)S2 - 12
108X-RAY DIFFRACTION108chain 'S' and (resseq 13:25)S13 - 25
109X-RAY DIFFRACTION109chain 'S' and (resseq 26:35)S26 - 35
110X-RAY DIFFRACTION110chain 'S' and (resseq 36:40)S36 - 40
111X-RAY DIFFRACTION111chain 'S' and (resseq 41:70)S41 - 70
112X-RAY DIFFRACTION112chain 'S' and (resseq 71:81)S71 - 81
113X-RAY DIFFRACTION113chain 'T' and (resseq 8:66)T8 - 66
114X-RAY DIFFRACTION114chain 'T' and (resseq 67:75)T67 - 75
115X-RAY DIFFRACTION115chain 'T' and (resseq 76:91)T76 - 91
116X-RAY DIFFRACTION116chain 'T' and (resseq 92:106)T92 - 106
117X-RAY DIFFRACTION117chain 'U' and (resseq 2:8)U2 - 8
118X-RAY DIFFRACTION118chain 'U' and (resseq 9:15)U9 - 15
119X-RAY DIFFRACTION119chain 'U' and (resseq 16:25)U16 - 25
120X-RAY DIFFRACTION120chain 'V' and (resseq 1:4)V1 - 4
121X-RAY DIFFRACTION121chain 'W' and (resseq 32:40)W32 - 40
122X-RAY DIFFRACTION122chain 'a' and (resseq 31:41)a31 - 41
123X-RAY DIFFRACTION123chain 'b' and (resseq 1:2)b1 - 2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more