[English] 日本語
Yorodumi
- PDB-5br8: Ambient-temperature crystal structure of 30S ribosomal subunit fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5br8
TitleAmbient-temperature crystal structure of 30S ribosomal subunit from Thermus thermophilus in complex with paromomycin
Components
  • (30S ribosomal protein ...) x 20
  • 16S ribosomal RNA
KeywordsRIBOSOME / 30S ribosomal subunit / Paromomycin / Ambient temperature / SFX / electrospinning
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 S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / 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
PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 ...PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSierra, R.G. / Gati, C. / Laksmono, H. / Dao, E.H. / Gul, S. / Fuller, F. / Kern, J. / Chatterjee, R. / Ibrahim, M. / Brewster, A. ...Sierra, R.G. / Gati, C. / Laksmono, H. / Dao, E.H. / Gul, S. / Fuller, F. / Kern, J. / Chatterjee, R. / Ibrahim, M. / Brewster, A. / Young, I.D. / Michels-Clark, T. / Aquila, A. / Mengning, L. / Hunter, M.S. / Koglin, J.E. / Boutet, S. / Junco, E.A. / Hayes, B. / Bogan, M.J. / Hampton, C.Y. / Puglisi, E.V. / Sauter, N.K. / Stan, C.A. / Zouni, A. / Yano, J. / Yachandra, V.K. / Soltis, S.M. / Puglisi, J.D. / DeMirci, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM51266 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082545 United States
CitationJournal: To Be Published
Title: Ambient-temperature crystal structure of 30S ribosomal subunit from Thermus thermophilus in complex with paromomycin
Authors: Sierra, R.G. / Gati, C. / Laksmono, H. / Dao, E.H. / Gul, S. / Fuller, F. / Kern, J. / Chatterjee, R. / Ibrahim, M. / Brewster, A. / Young, I.D. / Michels-Clark, T. / Aquila, A. / Mengning, ...Authors: Sierra, R.G. / Gati, C. / Laksmono, H. / Dao, E.H. / Gul, S. / Fuller, F. / Kern, J. / Chatterjee, R. / Ibrahim, M. / Brewster, A. / Young, I.D. / Michels-Clark, T. / Aquila, A. / Mengning, L. / Hunter, M.S. / Koglin, J.E. / Boutet, S. / Junco, E.A. / Hayes, B. / Bogan, M.J. / Hampton, C.Y. / Puglisi, E.V. / Sauter, N.K. / Stan, C.A. / Zouni, A. / Yano, J. / Yachandra, V.K. / Soltis, S.M. / Puglisi, J.D. / DeMirci, H.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Structure summary
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Feb 12, 2025Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S ribosomal RNA
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 type Z
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)794,735316
Polymers783,93521
Non-polymers10,800295
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area104270 Å2
ΔGint-865 kcal/mol
Surface area270870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)401.300, 401.300, 176.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
RNA chain , 1 types, 1 molecules A

#1: RNA chain 16S ribosomal RNA


Mass: 494169.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382

-
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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#6: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

-
Non-polymers , 4 types, 603 molecules

#22: Chemical
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: medication*YM
#23: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: Mg
#24: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 308 / 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: 4.59 Å3/Da / Density % sol: 73.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPD

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.29 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29 Å / Relative weight: 1
ReflectionResolution: 3.4→52.84 Å / Num. obs: 195895 / % possible obs: 100 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.29 / Net I/σ(I): 3
Reflection shellHighest resolution: 3.4 Å / Rmerge(I) obs: 0.87 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DR2

4dr2


Resolution: 3.4→52.84 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1413 0.72 %
Rwork0.1928 --
obs0.1931 195895 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→52.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19143 32504 541 308 52496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00656417
X-RAY DIFFRACTIONf_angle_d0.85983597
X-RAY DIFFRACTIONf_dihedral_angle_d20.27726590
X-RAY DIFFRACTIONf_chiral_restr0.0410505
X-RAY DIFFRACTIONf_plane_restr0.0044897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.52150.3571390.311319216X-RAY DIFFRACTION100
3.5215-3.66250.29071400.27519229X-RAY DIFFRACTION100
3.6625-3.82910.31821410.24919273X-RAY DIFFRACTION100
3.8291-4.03090.28081390.216719286X-RAY DIFFRACTION100
4.0309-4.28340.22711410.199919347X-RAY DIFFRACTION100
4.2834-4.61390.22431410.182419392X-RAY DIFFRACTION100
4.6139-5.07790.21631410.166819425X-RAY DIFFRACTION100
5.0779-5.81190.22651410.162719466X-RAY DIFFRACTION100
5.8119-7.31920.18541440.166719666X-RAY DIFFRACTION100
7.3192-52.83580.2121460.175520182X-RAY DIFFRACTION100
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)
10.3476-0.1627-0.09130.3390.1010.26720.0464-0.11920.0883-0.02920.04780.013-0.0199-0.0361-0.09820.6272-0.1013-0.01610.6803-0.08030.9913-116.46656.152232.2927
20.61590.23910.02461.11630.05790.41350.0873-0.2739-0.09380.58180.0318-0.27850.19150.2203-0.10581.14010.1665-0.32520.796-0.1490.949-70.7711-23.167453.6399
30.3232-0.9759-0.4052.05440.60540.07850.12650.126-0.40690.0976-0.19790.67820.0261-0.18380.08530.8248-0.08010.00060.9039-0.08351.1882-130.863336.515619.3533
44.92696.1031-6.69197.6774-8.35449.1371-0.51570.5313-1.91440.9138-0.3470.52162.951-0.96180.79743.4343-0.52840.75071.5918-0.47332.3757-88.2565-3.83711.4353
57.7545-0.6646-2.1574.1513-2.25282.0509-0.21411.14-2.0221-0.81690.6677-1.0098-0.40721.2362-0.27590.7002-0.37870.09551.8097-0.39841.2197-43.07743.20868.4124
63.8124-1.16122.04872.2615-2.95494.6285-0.18030.8960.6946-0.0355-0.0552-0.4856-1.29321.16840.3930.6772-0.32480.16491.1773-0.18171.7448-44.13549.407517.023
78.17771.55863.35232.0713-3.16189.5272-0.66610.652-0.86050.08370.2956-1.34981.18872.46960.25650.56060.1552-0.03920.9458-0.1011.5114-37.715132.603825.3564
82.0338-2.0893-2.04723.40730.50394.06660.2761-0.30910.04010.48610.3511-0.63990.13210.522-0.59410.8875-0.0246-0.46710.8594-0.37521.6531-42.861525.365937.2834
94.18042.1619-5.39559.292-3.28397.15970.6088-0.9723-1.48990.44910.1268-1.31422.92621.2508-0.72041.46880.2962-0.61081.2033-0.02671.817-38.2959.351939.2159
103.51871.442-1.14812.0753-2.37712.83630.14960.582-0.05810.10440.2499-0.5758-0.10350.987-0.28370.61-0.1408-0.02051.0891-0.43111.6786-43.770839.408825.9813
115.1477-2.7343-5.32762.7212.04765.99430.7122-0.2854-0.3020.12781.7406-2.4555-0.50322.8796-2.39351.09680.040.09633.0359-0.07962.5561-25.74236.528321.1686
121.65960.94451.09110.6921.37544.4003-0.03-0.46130.01050.54890.0633-0.542-0.65650.0633-0.02121.49810.2099-0.59610.9239-0.12250.871-57.714-6.271177.5961
136.42010.6641-1.0560.7951-0.93751.14250.1224-0.19660.14020.5266-0.29740.0436-0.4950.07530.11961.3448-0.0621-0.46750.8029-0.36631.1252-66.50789.197362.1014
149.3223.77574.74627.9592-1.19117.73510.7885-0.68620.87630.9019-0.2992-0.1346-0.56360.5359-0.45690.8115-0.05560.0180.8802-0.17020.7866-88.329345.6882.0467
151.86241.43970.99039.2578-6.84749.8288-0.1295-0.6788-0.30840.27430.3428-0.2450.90080.6719-0.18470.61030.1185-0.05531.0518-0.10810.8078-86.806639.576969.7962
162.1401-0.4664-3.29282.96550.07248.3950.0666-0.32790.13260.04850.4447-0.2399-0.11150.0307-0.4970.4253-0.0496-0.11780.8686-0.30280.9398-95.793663.572475.3179
175.51433.0745-1.59514.3554-1.59855.51640.6783-1.86060.70261.51730.0238-0.9340.19981.1239-0.61570.91220.0399-0.20931.3478-0.45280.9126-89.151767.661991.6298
184.4562-1.9502-2.36116.10024.27145.09230.00440.5923-0.44790.02630.8518-1.139-0.21541.2282-0.84290.4015-0.1203-0.11640.9063-0.01880.8484-85.70560.060967.6294
196.35553.6394-1.29253.75241.61593.68660.6678-1.44130.13071.2381-0.2737-1.24960.3091-0.0355-0.35361.1616-0.1913-0.28720.7135-0.18830.6297-73.057537.65352.6269
201.2581.83582.51984.10566.10839.25060.2202-0.1208-0.02610.2646-0.2686-0.24620.85751.28830.04040.8740.1314-0.33050.8064-0.19070.9382-77.824515.569341.9574
214.83365.08653.03815.46253.91056.4795-0.2271-0.53170.28080.40620.2996-1.4202-0.17330.4227-0.28740.38890.0235-0.22690.685-0.26751.2184-70.460437.58549.0703
223.59252.39690.05014.2866-4.10946.4346-0.0304-0.25390.15230.1923-0.4767-1.30050.28390.90290.48390.54960.3319-0.28790.9202-0.43881.1876-66.666831.774349.8141
237.0887-0.05224.18071.0215-2.16326.9218-0.316-0.15860.91230.05750.5015-1.118-0.99870.647-0.23070.7559-0.2152-0.10810.715-0.35481.2831-70.821654.200744.9692
243.8583.73834.36883.92225.31098.8248-0.35840.4895-0.3617-0.8935-0.80661.63820.1056-0.85611.17940.7406-0.1548-0.10140.5653-0.08211.5317-80.040647.028133.7638
254.3418-1.9596-3.00783.7057-0.78663.71860.2327-0.4280.1180.3397-0.17950.1379-0.57740.14410.08270.3448-0.0549-0.09910.737-0.38420.9547-83.305953.823145.5282
266.62880.37260.34872.9478-1.23050.58550.0991-0.29120.2090.3452-0.1297-0.167-0.0257-0.069-0.00570.5714-0.0243-0.09580.5094-0.18030.6484-79.350446.179244.1042
272.39180.91770.32542.9902-3.97556.4122-0.98260.37110.845-0.21510.3662-1.5454-1.64441.40140.58920.8334-0.3099-0.15011.0726-0.42491.3857-66.229863.076835.0778
284.978-0.86161.24082.2721.63563.49170.10830.91580.7047-0.5494-0.3466-0.06920.050.59320.28531.5207-0.33640.07251.04090.15440.4165-86.13125.9366-48.9802
297.4742-4.3353-1.04147.7097-2.40188.77650.16090.3526-0.0614-1.41410.3627-0.2319-0.0539-0.1295-0.50991.1477-0.2528-0.02260.6174-0.1260.6662-85.278424.943-42.6111
305.1102-3.72956.15754.9856-3.99669.3106-0.95411.90822.24790.3195-0.7617-2.2553-0.92351.21111.59451.4183-0.59050.32151.05320.14861.3575-69.074833.9858-29.1386
312.32370.1482-1.32845.343-0.70930.8312-0.0408-0.16492.77-0.79220.3523-5.3048-0.49610.9327-0.28620.9594-0.0420.14351.1473-0.19781.9541-57.8208-17.94220.2881
325.4193-5.064-6.58045.70585.11259.091-0.7081-1.0956-0.7969-0.0965-1.1580.1172-0.8994-0.80191.83160.65950.1462-0.31640.9179-0.20591.5127-48.6521-40.019818.415
335.5393.545-3.36342.7585-2.97228.59520.34350.1526-0.6253-0.2942-0.94050.2542-0.15350.38150.65240.93650.2244-0.40560.6682-0.21451.2955-58.0662-45.508620.7348
340.64151.0218-0.07592.2008-0.81270.8448-0.00860.4977-0.2961-1.0021-0.5499-0.00460.4872-0.29550.41571.64130.66580.07341.2038-0.62961.9496-54.3412-54.05636.4197
359.3501-6.80264.99786.9523-6.29226.3079-0.48020.03990.5133-0.39310.1443-0.63120.38-0.40350.30751.2226-0.12630.01260.7188-0.39370.8436-64.8707-33.36246.2349
366.9359-2.1144.91245.9608-4.30965.1814-1.3757-2.97782.31982.02471.6214-1.1829-0.5811-1.4654-0.34431.36010.103-0.14241.1409-0.21030.9368-76.5216-19.6015.3931
374.15492.968-0.74092.9662-1.58761.5167-0.09980.04790.96330.52620.15031.2022-0.51740.0544-0.08470.95480.2784-0.18210.6875-0.20461.2514-65.5509-35.238313.0049
384.93385.8382-5.63197.4548-5.87958.82650.0761-0.4367-0.3358-0.8988-0.017-0.85350.76510.00110.06240.77910.112-0.16420.8178-0.40081.4948-67.1086-50.807313.1779
399.6263-1.46313.73063.6107-5.7639.4156-0.1750.5013-0.1915-1.9718-0.52631.8154-0.0155-2.35410.68660.97010.0981-0.26461.0274-0.24280.82-72.6781-37.85453.5439
401.96342.64582.46043.61953.55714.1518-0.2479-1.2275-0.31283.01991.4301-4.03370.02552.6725-1.13961.48690.0212-0.6251.2425-0.09121.7443-75.7252-19.6581-0.2224
416.7547-2.5159-2.67620.93670.9991.19850.07960.4322-0.2312-0.1340.64550.03010.21860.1627-0.72160.6441-0.1740.02390.4584-0.07851.1299-77.344859.611913.8716
427.5233-4.8685.25294.6717-1.67135.66310.24490.2029-0.5504-0.91270.4232-0.01160.84280.2506-0.59170.6744-0.11560.21170.522-0.15671.3307-67.824460.549312.6772
436.87782.86686.18974.84613.99437.2808-0.2794-0.08051.33890.0899-0.2460.5865-1.07650.58610.53180.619-0.41110.31770.6512-0.26791.3036-74.27973.061716.9826
443.1072-0.93631.43551.9524-2.66875.0377-0.23120.43941.05170.0728-0.2578-0.6428-1.0521.06540.43880.5611-0.15390.03780.573-0.03351.3769-67.027869.249714.6125
452.9888-1.74062.17321.6672-1.95366.15610.21790.01780.0522-0.7063-0.0164-0.23220.20050.156-0.17940.5873-0.22360.2220.60320.03511.095-68.372866.24885.9559
461.3595-1.1256-0.17625.7982-3.75253.14390.6359-0.4755-0.53950.6072-0.07220.11170.2999-0.1057-0.54460.7551-0.2629-0.27230.7317-0.18671.1488-59.964154.174827.541
479.6219-8.0637.28547.1172-5.43766.8030.20860.0769-0.78150.13170.01890.3453-0.34340.2997-0.24090.5484-0.09690.11290.7608-0.19781.3384-70.718556.330825.9159
481.95820.87052.6813.65042.04393.8961-0.47490.2157-0.2459-0.31530.11070.06530.9494-0.73970.14160.6843-0.30190.14060.5398-0.0661.061-91.117665.680120.2547
494.726-0.31244.13033.4725-2.33585.35010.5295-0.39182.0320.4148-0.99121.9772-1.2526-0.94530.49981.15640.1277-0.12740.5602-0.18960.8758-90.106874.365732.1885
503.5043-1.79633.72634.37890.57755.748-1.1486-2.39190.23523.23880.81122.0889-2.9154-1.53040.37091.09490.21240.14931.0074-0.10650.9917-80.66565.532136.1047
517.0343-2.44495.24190.9186-1.81794.43-0.3482-0.47580.11830.8329-0.2050.5283-0.2738-0.28380.49990.6208-0.17140.2280.736-0.33011.0067-81.145473.342725.5871
522.17911.912-0.62635.9476-2.86454.59420.405-0.3955-0.32011.5535-0.7726-0.882-0.1671-0.01890.32670.7742-0.26290.14720.5354-0.38241.3321-80.014677.132928.9707
538.0317-3.7961.05594.26942.54423.9333-0.4875-0.049-0.29360.10750.4031.26140.09420.04540.05880.6292-0.2080.20490.5142-0.0810.9556-82.702368.450325.556
543.62972.7822.61112.15551.63127.5688-0.9318-0.54370.62820.42690.671-1.26630.33811.39330.29730.9010.2703-0.38241.2491-0.35691.8767-33.9204-40.122738.5951
552.4794-2.53074.15662.6445-3.99697.92960.2412-0.1379-0.6785-0.3978-0.42770.22150.1885-0.00340.11810.97070.3312-0.61991.28980.18221.8963-39.0451-50.358639.2894
563.9432-4.00961.27087.45491.99174.6825-0.48611.28680.08070.6009-0.41730.7597-0.5867-0.69350.88230.91590.3442-0.29960.9657-0.24481.2087-42.3693-45.515829.9196
574.9234.4824-0.46416.813-5.00757.8237-0.0808-1.0886-0.0937-0.5-0.0889-0.32330.7531.40560.24530.65570.3183-0.24750.8971-0.2461.2126-36.018-40.221834.8165
584.0812-3.49343.30292.9934-2.83982.741-0.1138-0.26732.29390.38330.1137-0.8862-1.2928-0.6066-0.05251.05620.47270.071.3627-0.2942.2567-28.477-30.611826.1831
593.22590.7679-0.52450.5304-1.01872.5617-0.3291-0.5045-0.2833-0.19790.2823-0.57830.80080.2604-0.011.19340.2124-0.46820.7604-0.23951.4795-53.1298-26.510837.4664
604.89982.8935-4.87089.9584-0.12517.3850.51772.16051.2592-0.0095-0.90550.2806-0.5687-1.4790.41311.20530.3259-0.42781.0417-0.11680.8664-76.2-23.137637.3299
619.1139-7.29344.10478.3168-5.75236.38970.3266-0.68350.96520.4438-0.3675-0.77710.41471.55120.03131.24290.2406-0.48611.3705-0.36521.3926-37.1753-22.948170.3038
624.55512.8532-1.43483.2378-3.78327.0534-0.3419-1.60350.48810.5459-0.3472-0.9578-0.28241.30870.90341.36260.5448-0.88771.5171-0.26881.7948-33.8665-28.906966.7309
634.73921.0766-3.16096.7093.19864.48181.1645-0.3212-0.1919-0.8567-0.5910.04391.46650.523-0.59661.85490.3678-0.09930.7767-0.08351.9293-57.8692-25.83361.1192
645.3984-6.4626-0.33749.6391-1.09721.2825-0.9896-0.57721.6450.7456-0.1396-0.6581-0.32920.01381.13911.17840.1241-0.27831.0604-0.29660.8987-64.4003-18.887157.2018
656.99861.69811.69126.299-0.62446.7620.2933-1.6701-0.71650.3624-0.9481-0.9584-0.00661.14810.78541.58820.5825-0.92792.04190.0531.6459-30.3931-32.3273.9782
664.84964.01512.16224.01373.64685.95550.32320.213-0.58490.6529-0.1534-0.58570.46330.5405-0.37032.0936-0.1399-1.08632.0952-0.64321.7756-28.1907-25.414283.2482
678.6074-0.5757-2.35360.03720.15630.64250.0022-2.3491-1.35964.26421.1077-2.47410.27521.607-0.9272.76920.4618-1.06651.2932-0.33491.6854-39.5885-16.833978.7958
683.01243.34781.97724.0013.44926.89590.11830.2794-0.3320.1805-0.5806-1.0861.16571.53260.4961.5206-0.0661-0.43081.75590.48871.4136-42.8128-29.261875.9881
696.47641.8473-4.33727.7708-4.67236.56150.84150.2631-0.2553-1.0775-0.1259-0.5335-0.86280.7902-0.7480.78560.1419-0.0610.7407-0.2991.0941-82.5785-13.3119-25.0144
702.19430.8301-0.98439.4274-5.91363.81550.51820.0521-0.08450.03480.25050.83470.54190.4504-0.69750.6677-0.0045-0.04690.8964-0.26161.0433-86.1872-17.3767-18.3272
719.4353-5.338-6.57124.02765.22616.8272-0.1899-0.204-0.9716-0.52340.15740.19631.23590.833-0.10911.0260.035-0.01280.5437-0.06920.952-79.1843-21.3875-20.277
728.39-3.30970.80929.2741-2.38284.30860.18260.28120.50070.00930.2246-1.61250.30010.5399-0.39150.74610.08680.08830.5384-0.16420.8466-75.1929-11.6073-20.6288
732.0129-1.50711.00432.27671.93167.44160.6251.2076-0.1667-1.99020.1245-3.4831-0.95161.136-0.74710.8376-0.20690.3870.69-0.18461.3372-71.5509-11.2233-25.6687
747.2224-0.9219-2.90883.4808-2.33073.3770.163-0.191-0.3148-0.42590.17530.8350.0401-0.172-0.37550.5937-0.1663-0.08650.8415-0.23241.1126-90.30636.0843-13.1429
758.25317.2148-7.04836.3989-6.20916.0329-0.10910.02960.5553-0.30560.64490.2173-0.0109-0.1977-0.53620.52660.0685-0.01680.6094-0.06940.7497-110.879246.55831.0865
763.2505-1.4181.52045.04861.2552.9980.0611-0.1467-0.7508-0.1874-0.1670.62150.5831-0.44780.05040.7185-0.14620.06450.46890.12491.0878-120.79925.803955.4628
778.97332.79310.66423.8167-3.66628.61540.79691.2852.12441.1062-0.43893.2958-0.9507-1.309-0.45181.28250.1225-0.20610.7006-0.14082.0842-85.5736-73.540235.4073
786.5176.2322-4.72446.5011-4.95274.8191-0.0314-0.03910.0228-0.3783-0.0864-0.63810.4578-0.020.1541.0992-0.3195-0.38460.50970.31251.1521-80.9179-68.436638.369
796.9043-2.2769-3.87771.66152.82624.949-0.2743-0.6456-0.98580.2726-0.06740.21391.23230.45680.36271.62020.1969-0.47620.67360.11841.3303-79.1184-75.850842.1285
806.2104-6.1466-4.4416.66395.645.8692-1.2971-1.8135-2.30392.47581.16141.62071.66010.36880.14741.36960.07320.04220.92180.33380.9762-96.1104-65.104653.165
819.28091.9051-1.13069.549-9.50049.51610.2724-0.42240.1194-0.0203-0.14450.4705-0.61390.0916-0.14761.29750.1123-0.0420.5716-0.16061.1318-101.1684-49.423658.4228
824.9027-4.1541-1.35834.58580.58440.67080.5464-0.10920.0251-0.0168-0.5650.4272-0.3492-0.20460.02471.1877-0.1801-0.10720.6717-0.14550.8228-96.8197-40.294847.0728
837.52413.3176-6.54956.3515-2.51235.72940.6133-1.2985-1.20040.45190.0066-0.00912.84711.3868-0.55971.71940.0313-0.56991.2260.18491.1371-82.0719-20.882578.5388
841.13431.7725-0.44535.7092-0.31960.22254.01-4.47850.61236.2841-3.2429-3.57294.4289-1.118-0.81151.7319-0.2826-0.37362.05840.12781.6261-80.2211-32.856983.8798
853.7491-0.9042.0859.4216-0.44461.4590.0659-0.1581-0.7313-1.52380.34790.1492-0.3803-0.1589-0.43691.52110.5611-0.29391.5596-0.30610.8078-78.0016-28.825574.5597
868.7108-4.90835.99542.8117-3.43164.22930.4536-0.79120.26120.5312-0.1036-0.580.6778-1.1911-0.28071.56470.1056-0.09081.0584-0.12680.929-74.239-16.13170.8651
875.4733-1.202-2.97533.5609-2.44994.6393-0.0926-0.1532-0.18660.65310.0444-1.0360.014-0.18160.06810.94890.0747-0.33170.6469-0.21410.843-65.0903-17.271264.0278
882.40820.0395-0.82635.57275.49645.73980.49640.94420.453-1.35870.2867-1.8142-1.8081.3347-0.81161.1079-0.23890.00410.88210.08921.1505-89.771958.2249-29.4414
897.74425.14284.1627.123.68214.89560.30770.16940.18690.1972-0.08390.2261-0.22810.5552-0.21540.8509-0.05950.28130.6196-0.03730.7246-96.054154.7824-21.7953
906.42871.1646-1.05978.92180.98976.76250.7374-0.48440.36852.0879-0.45770.2504-0.0887-0.2583-0.27990.8507-0.0582-0.02620.57680.08390.8244-98.341756.0452-11.509
916.06753.57114.06946.13846.9867.9560.3593-0.52680.67070.1657-0.70152.7016-0.9181-2.55710.28520.70350.13830.28271.07630.24491.5596-102.268868.4477-19.0195
922.19341.5204-0.79536.70650.10970.4148-0.059-0.9880.4650.2456-0.1892-1.3694-0.068-0.16060.2050.5722-0.0738-0.09670.8522-0.32761.0901-122.858482.11959.9209
930.9486-0.1762-2.28523.46590.11536.52760.4522-0.07020.39420.04020.1005-0.9323-0.5313-0.0508-0.60690.57620.02580.05380.7886-0.26571.2398-122.562384.547355.3672
941.9643-4.11584.3738.6463-9.20079.802-0.3481-0.04390.88411.1927-0.0776-1.1731-1.49171.22660.44530.9384-0.1839-0.09761.0243-0.58691.5586-113.342689.806865.2679
950.5391-1.439-0.74064.44322.90375.5168-0.09850.1340.2826-0.03650.8148-1.1824-0.52881.0597-0.69440.7052-0.22180.34190.6703-0.44441.7441-120.347298.444750.2733
963.92720.42551.58936.018-4.11654.9099-0.5059-0.94341.88771.7547-0.08170.9074-0.40840.06260.44590.82980.09540.09771.0899-0.57091.5985-124.553998.454561.197
978.75843.14114.61785.64653.24466.440.11451.01440.4089-0.20750.1391-0.5779-0.1140.498-0.21660.52180.0550.23740.50840.10150.8871-119.154879.28476.556
987.9585-5.70894.66116.957-3.73843.190.070.71010.34630.1479-0.1531-0.007-0.43620.09260.06880.63640.08560.2670.6446-0.03520.8514-115.338177.30849.2968
999.50867.5998-7.4816.0744-5.96326.013-0.60230.8579-0.9324-1.63670.7686-0.40251.1748-0.0258-0.10450.94980.0588-0.12770.8195-0.18860.6863-114.431361.13950.6369
1009.26116.65670.55684.98431.15313.2974-0.33660.3007-0.3216-0.0728-0.1078-2.09940.6441.82760.48670.9094-0.14550.18612.0714-0.6321.24-60.812418.9018-19.8204
1019.66610.7463.8284.6386-3.82915.24570.77740.5195-0.4944-0.5076-0.43720.86180.5119-0.3586-0.32571.340.0027-0.08131.4924-0.30471.7422-59.934524.4057-27.8091
1028.50631.340.32747.1303-2.71914.6993-0.40730.7353-1.50720.7547-0.5153-0.15551.2339-0.31470.83551.3191-0.19930.37690.8462-0.18151.3022-71.675627.1246-32.3639
1031.4031-1.25262.00274.7057-6.60039.3135-0.03921.0505-0.8002-1.34930.366-2.46731.04412.6688-0.44020.7143-0.1260.29060.9867-0.55071.4954-67.972418.1888-30.0177
1044.94936.92034.00969.80695.59073.2502-0.720.1903-1.12490.05751.0106-1.19861.23441.1047-0.28431.09330.03910.08560.9936-0.03051.0745-72.30412.9839-21.7179
1057.9984.91122.91378.37787.12219.42680.4363-0.11610.1450.59070.7753-0.3856-0.22280.952-1.14290.742-0.07710.20920.7562-0.10270.6555-73.692323.8171-22.6853
1064.25394.0787-0.76636.0069-2.79592.2030.90250.051-0.8152-0.8456-0.5586-0.08860.95191.4609-0.40791.02130.1968-0.11061.1115-0.25521.0163-75.13296.5327-26.7096
1078.3499-5.2194-6.15295.29196.16899.25270.21061.8020.9647-1.90830.01391.3565-2.7372-2.4259-0.26742.01110.0268-0.44311.0320.451.215-86.6333-52.409371.7378
1085.38795.2466-5.32975.2017-5.25575.31860.6518-2.07250.18641.9381-1.3320.3365-1.33661.0850.62491.947-0.24110.0381.1153-0.02030.8785-99.711-51.765186.6775
1099.2563-3.67077.29924.6195-6.06849.37820.352-0.02421.14682.1542-0.09033.2546-2.562-0.8159-0.34021.78920.2110.20840.8894-0.10551.5951-105.9139-46.572481.9206
1104.071.87545.84051.11312.55678.45330.4906-1.2656-0.42382.3593-0.3295-0.582-0.5640.0504-0.12562.32050.1764-0.1420.99790.09450.8055-94.9274-47.673773.8432
1119.1486-6.08984.04744.9074-4.57296.9643-0.2277-0.40590.09741.9562-0.47660.16120.3010.46110.76291.4452-0.1682-0.03150.89420.06560.8795-103.0663-50.404173.5672
1127.1081-6.0225.37419.0797-6.32194.8595-0.6013-1.059-0.89640.34141.8610.6049-0.6474-2.2388-1.23981.080.0625-0.05861.4550.08290.9181-102.4924-41.472362.71
1132.87032.2005-3.80821.6855-3.08988.2813-0.07090.08270.2787-0.0657-0.0539-0.10290.0077-0.40190.10160.50920.09430.13480.8446-0.20541.1941-157.778392.072325.1215
1143.35493.08382.18997.6704-1.31223.7168-0.3576-1.02280.3531-0.25220.4784-2.2307-0.21230.6445-0.10890.70560.06320.01331.05470.01561.3627-147.908894.328229.8823
1156.898-4.24096.73412.883-4.41937.90390.41210.40920.5424-0.6404-0.427-0.05751.75271.778-0.04021.10140.31770.47630.78020.01161.5324-147.458196.520313.4012
1169.94525.85567.89225.77544.836.2777-0.2766-0.5893-0.00460.3339-0.6274-0.3478-0.7402-0.01660.83871.1443-0.12280.03840.91170.35360.887-151.7715106.99455.8399
1175.54814.52225.66744.95645.44958.68581.5723-6.4361-1.86463.4846-2.6925-2.16771.82472.65171.18081.45380.0382-0.21341.77740.33551.3199-75.6146-51.97446.1005
1183.95080.2602-2.21545.36260.44143.1871-0.1651-0.12450.0835-0.03070.40310.22360.18460.1134-0.23611.3958-0.02590.13751.6358-0.14742.4048-70.5908-48.427747.8403
1197.96193.1642-1.35725.86081.80471.42410.7748-2.5669-3.23262.7351-0.2028-1.78692.61221.7915-0.54122.17020.3561-0.53721.50610.34551.6567-66.7422-54.280153.6141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:920)
2X-RAY DIFFRACTION2chain 'A' and (resseq 921:1400)
3X-RAY DIFFRACTION3chain 'A' and (resseq 1401:1532)
4X-RAY DIFFRACTION4chain 'A' and (resseq 1533:1541)
5X-RAY DIFFRACTION5chain 'B' and (resseq 7:25)
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:64)
7X-RAY DIFFRACTION7chain 'B' and (resseq 65:86)
8X-RAY DIFFRACTION8chain 'B' and (resseq 87:122)
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:148)
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:226)
11X-RAY DIFFRACTION11chain 'B' and (resseq 227:240)
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:112)
13X-RAY DIFFRACTION13chain 'C' and (resseq 113:207)
14X-RAY DIFFRACTION14chain 'D' and (resseq 2:34)
15X-RAY DIFFRACTION15chain 'D' and (resseq 35:67)
16X-RAY DIFFRACTION16chain 'D' and (resseq 68:148)
17X-RAY DIFFRACTION17chain 'D' and (resseq 149:181)
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:14)
20X-RAY DIFFRACTION20chain 'E' and (resseq 15:27)
21X-RAY DIFFRACTION21chain 'E' and (resseq 28:50)
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:63)
23X-RAY DIFFRACTION23chain 'E' and (resseq 64:79)
24X-RAY DIFFRACTION24chain 'E' and (resseq 80:86)
25X-RAY DIFFRACTION25chain 'E' and (resseq 87:103)
26X-RAY DIFFRACTION26chain 'E' and (resseq 104:140)
27X-RAY DIFFRACTION27chain 'E' and (resseq 141:154)
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:32)
29X-RAY DIFFRACTION29chain 'F' and (resseq 33:92)
30X-RAY DIFFRACTION30chain 'F' and (resseq 93:101)
31X-RAY DIFFRACTION31chain 'G' and (resseq 2:11)
32X-RAY DIFFRACTION32chain 'G' and (resseq 12:20)
33X-RAY DIFFRACTION33chain 'G' and (resseq 21:52)
34X-RAY DIFFRACTION34chain 'G' and (resseq 53:57)
35X-RAY DIFFRACTION35chain 'G' and (resseq 58:79)
36X-RAY DIFFRACTION36chain 'G' and (resseq 80:92)
37X-RAY DIFFRACTION37chain 'G' and (resseq 93:109)
38X-RAY DIFFRACTION38chain 'G' and (resseq 110:129)
39X-RAY DIFFRACTION39chain 'G' and (resseq 130:144)
40X-RAY DIFFRACTION40chain 'G' and (resseq 145:156)
41X-RAY DIFFRACTION41chain 'H' and (resseq 1:18)
42X-RAY DIFFRACTION42chain 'H' and (resseq 19:29)
43X-RAY DIFFRACTION43chain 'H' and (resseq 30:41)
44X-RAY DIFFRACTION44chain 'H' and (resseq 42:53)
45X-RAY DIFFRACTION45chain 'H' and (resseq 54:62)
46X-RAY DIFFRACTION46chain 'H' and (resseq 63:72)
47X-RAY DIFFRACTION47chain 'H' and (resseq 73:85)
48X-RAY DIFFRACTION48chain 'H' and (resseq 86:95)
49X-RAY DIFFRACTION49chain 'H' and (resseq 96:100)
50X-RAY DIFFRACTION50chain 'H' and (resseq 101:106)
51X-RAY DIFFRACTION51chain 'H' and (resseq 107:116)
52X-RAY DIFFRACTION52chain 'H' and (resseq 117:127)
53X-RAY DIFFRACTION53chain 'H' and (resseq 128:138)
54X-RAY DIFFRACTION54chain 'I' and (resseq 2:25)
55X-RAY DIFFRACTION55chain 'I' and (resseq 26:32)
56X-RAY DIFFRACTION56chain 'I' and (resseq 33:53)
57X-RAY DIFFRACTION57chain 'I' and (resseq 54:88)
58X-RAY DIFFRACTION58chain 'I' and (resseq 89:97)
59X-RAY DIFFRACTION59chain 'I' and (resseq 98:117)
60X-RAY DIFFRACTION60chain 'I' and (resseq 118:128)
61X-RAY DIFFRACTION61chain 'J' and (resseq 3:29)
62X-RAY DIFFRACTION62chain 'J' and (resseq 30:42)
63X-RAY DIFFRACTION63chain 'J' and (resseq 43:47)
64X-RAY DIFFRACTION64chain 'J' and (resseq 48:70)
65X-RAY DIFFRACTION65chain 'J' and (resseq 71:78)
66X-RAY DIFFRACTION66chain 'J' and (resseq 79:85)
67X-RAY DIFFRACTION67chain 'J' and (resseq 86:93)
68X-RAY DIFFRACTION68chain 'J' and (resseq 94:100)
69X-RAY DIFFRACTION69chain 'K' and (resseq 11:34)
70X-RAY DIFFRACTION70chain 'K' and (resseq 35:57)
71X-RAY DIFFRACTION71chain 'K' and (resseq 58:75)
72X-RAY DIFFRACTION72chain 'K' and (resseq 76:100)
73X-RAY DIFFRACTION73chain 'K' and (resseq 101:110)
74X-RAY DIFFRACTION74chain 'K' and (resseq 111:126)
75X-RAY DIFFRACTION75chain 'L' and (resseq 5:32)
76X-RAY DIFFRACTION76chain 'L' and (resseq 33:128)
77X-RAY DIFFRACTION77chain 'M' and (resseq 2:14)
78X-RAY DIFFRACTION78chain 'M' and (resseq 15:21)
79X-RAY DIFFRACTION79chain 'M' and (resseq 22:61)
80X-RAY DIFFRACTION80chain 'M' and (resseq 62:83)
81X-RAY DIFFRACTION81chain 'M' and (resseq 84:93)
82X-RAY DIFFRACTION82chain 'M' and (resseq 94:119)
83X-RAY DIFFRACTION83chain 'N' and (resseq 2:11)
84X-RAY DIFFRACTION84chain 'N' and (resseq 12:16)
85X-RAY DIFFRACTION85chain 'N' and (resseq 17:24)
86X-RAY DIFFRACTION86chain 'N' and (resseq 25:29)
87X-RAY DIFFRACTION87chain 'N' and (resseq 30:61)
88X-RAY DIFFRACTION88chain 'O' and (resseq 2:15)
89X-RAY DIFFRACTION89chain 'O' and (resseq 16:49)
90X-RAY DIFFRACTION90chain 'O' and (resseq 50:73)
91X-RAY DIFFRACTION91chain 'O' and (resseq 74:88)
92X-RAY DIFFRACTION92chain 'P' and (resseq 1:19)
93X-RAY DIFFRACTION93chain 'P' and (resseq 20:43)
94X-RAY DIFFRACTION94chain 'P' and (resseq 44:52)
95X-RAY DIFFRACTION95chain 'P' and (resseq 53:62)
96X-RAY DIFFRACTION96chain 'P' and (resseq 63:83)
97X-RAY DIFFRACTION97chain 'Q' and (resseq 2:17)
98X-RAY DIFFRACTION98chain 'Q' and (resseq 18:82)
99X-RAY DIFFRACTION99chain 'Q' and (resseq 83:100)
100X-RAY DIFFRACTION100chain 'R' and (resseq 19:23)
101X-RAY DIFFRACTION101chain 'R' and (resseq 24:28)
102X-RAY DIFFRACTION102chain 'R' and (resseq 29:36)
103X-RAY DIFFRACTION103chain 'R' and (resseq 37:43)
104X-RAY DIFFRACTION104chain 'R' and (resseq 44:52)
105X-RAY DIFFRACTION105chain 'R' and (resseq 53:76)
106X-RAY DIFFRACTION106chain 'R' and (resseq 77:88)
107X-RAY DIFFRACTION107chain 'S' and (resseq 2:12)
108X-RAY DIFFRACTION108chain 'S' and (resseq 13:25)
109X-RAY DIFFRACTION109chain 'S' and (resseq 26:35)
110X-RAY DIFFRACTION110chain 'S' and (resseq 36:40)
111X-RAY DIFFRACTION111chain 'S' and (resseq 41:70)
112X-RAY DIFFRACTION112chain 'S' and (resseq 71:81)
113X-RAY DIFFRACTION113chain 'T' and (resseq 8:66)
114X-RAY DIFFRACTION114chain 'T' and (resseq 67:75)
115X-RAY DIFFRACTION115chain 'T' and (resseq 76:91)
116X-RAY DIFFRACTION116chain 'T' and (resseq 92:106)
117X-RAY DIFFRACTION117chain 'U' and (resseq 2:8)
118X-RAY DIFFRACTION118chain 'U' and (resseq 9:15)
119X-RAY DIFFRACTION119chain 'U' and (resseq 16:25)

+
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