[English] 日本語
Yorodumi
- PDB-4dr2: Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dr2
TitleCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with multiple copies of paromomycin molecules bound
Components
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
KeywordsRIBOSOME/ANTIBIOTIC / decoding / Streptomycin / RNA structure / antibiotic resistance / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / 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 S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / 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 S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / K homology (KH) domain / Double Stranded RNA Binding Domain - #20 / Helicase, Ruva Protein; domain 3 - #50 / 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 / Double Stranded RNA Binding Domain / Ribosomal protein S14, type Z / 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 S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / 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 S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / 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 / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Few Secondary Structures / Irregular / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S17, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site
Similarity search - Domain/homology
PAROMOMYCIN / : / 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 ...PAROMOMYCIN / : / 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: 3.249 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

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)802,334361
Polymers783,93621
Non-polymers18,398340
Water9,674537
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)402.596, 402.596, 177.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
RNA chain , 1 types, 1 molecules A

#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

-
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 / Ribosome


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, 877 molecules

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


Mass: 615.628 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#23: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 321 / Source method: obtained synthetically / 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 / Water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.59 Å3/Da / Density % sol: 73.2 %
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: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2008
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 10.77 / Number: 843275 / Rmerge(I) obs: 0.115 / Χ2: 1.06 / D res high: 3.25 Å / D res low: 45 Å / Num. obs: 226409 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.994597.210.0411.0123.6
5.556.9999.610.0791.0933.7
4.855.5599.810.0871.0193.7
4.414.8599.910.1031.0423.7
4.094.4110010.1391.0883.7
3.854.0910010.1991.073.7
3.663.8510010.2731.0933.8
3.53.6610010.4011.0863.8
3.373.510010.5761.0663.8
3.253.3710010.8111.0553.8
ReflectionResolution: 3.249→45 Å / Num. all: 226409 / Num. obs: 226409 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.115 / Χ2: 1.063 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.249-3.373.80.811224441.0551100
3.37-3.53.80.576225111.0661100
3.5-3.663.80.401225201.0861100
3.66-3.853.80.273225741.0931100
3.85-4.093.70.199225631.071100
4.09-4.413.70.139226291.0881100
4.41-4.853.70.103226651.042199.9
4.85-5.553.70.087227321.019199.8
5.55-6.993.70.079228391.093199.6
6.99-453.60.041229321.012197.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_978refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHENIXdev_978phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.249→44.389 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8659 / SU ML: 0.37 / σ(F): 1.34 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 11411 5.04 %FROM PDB ENTRY 2VQE
Rwork0.1711 ---
obs0.1731 226222 99.61 %-
all-226222 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.454 Å2 / ksol: 0.268 e/Å3
Displacement parametersBiso max: 585.54 Å2 / Biso mean: 98.2273 Å2 / Biso min: 28.81 Å2
Baniso -1Baniso -2Baniso -3
1--8.6416 Å2-0 Å20 Å2
2---8.6416 Å20 Å2
3---17.2833 Å2
Refinement stepCycle: LAST / Resolution: 3.249→44.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19143 32504 1037 537 53221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00757138
X-RAY DIFFRACTIONf_angle_d1.03284725
X-RAY DIFFRACTIONf_chiral_restr0.06810714
X-RAY DIFFRACTIONf_plane_restr0.0064897
X-RAY DIFFRACTIONf_dihedral_angle_d24.78927624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.249-3.28590.35533940.298371137507100
3.2859-3.32460.28333720.271870887460100
3.3246-3.36510.29463980.257370847482100
3.3651-3.40770.28993760.249171677543100
3.4077-3.45250.26693800.241870537433100
3.4525-3.49980.27954060.238971177523100
3.4998-3.54980.25523930.216971607553100
3.5498-3.60270.26024000.210370677467100
3.6027-3.6590.24353660.203771227488100
3.659-3.7190.22354050.194170927497100
3.719-3.7830.23513950.184271447539100
3.783-3.85180.21753450.182671747519100
3.8518-3.92580.23523800.176371337513100
3.9258-4.00590.19733610.172271627523100
4.0059-4.0930.20614130.161371097522100
4.093-4.18810.18283560.151471887544100
4.1881-4.29280.19813790.147671407519100
4.2928-4.40870.18464050.145271427547100
4.4087-4.53830.17683970.143771727569100
4.5383-4.68470.20283550.145272047559100
4.6847-4.85190.19443440.141271887532100
4.8519-5.04590.18133930.136371607553100
5.0459-5.27520.17833620.138172117573100
5.2752-5.55280.18613800.135572107590100
5.5528-5.90.17723850.13572357620100
5.9-6.35430.18943470.139472497596100
6.3543-6.99160.18493750.13787231760699
6.9916-7.99820.18143680.14017245761399
7.9982-10.05750.19773990.16697217761698
10.0575-44.3930.23233820.21877234761694
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.21870.0916-0.07580.1896-0.05630.14540.06010.05980.00650.0720.0420.060.08630.026600.4410.02890.05480.42090.01510.4733144.849884.4511-11.5033
20.3693-0.0651-0.1368-0.36340.0799-0.01640.2642-0.33510.0431-0.54830.00570.2784-0.07730.150.3188-0.1189-0.23570.38510.8932-0.27090.2866224.6299130.50889.6093
30.1667-0.0243-0.1030.0262-0.11490.1775-0.0630.0051-0.1959-0.02970.0902-0.18260.13650.139900.47160.06360.02230.5411-0.0130.5978166.492671.8481-24.3951
40.00890.00840.00760.00590.00760.00660.0375-0.0509-0.0143-0.09710.04730.11840.055-0.0297-00.80390.10120.20140.55640.14311.067153.5939157.3685-30.2277
50.01130.0030.00880.0070.00040.00250.0101-0.00370.0377-0.03120.0086-0.0083-0.03750.059600.3663-0.07650.27340.214-0.09420.6545169.0298160.5568-15.4503
60.00570.00250.00050.00650.00070.006-0.0401-0.05050.04920.06740.0410.0175-0.01130.046600.7976-0.23850.21770.9343-0.33890.9833187.3689161.2175-3.5417
70.02980.00890.02910.0059-0.00020.0244-0.107-0.08660.0858-0.06270.0963-0.0103-0.05590.012200.80460.01870.23370.3267-0.01151.0078162.216159.8008-18.862
80.0642-0.0023-0.00660.00950.03210.0397-0.01160.1613-0.00960.07120.044-0.0603-0.0381-0.02160.01850.7636-0.15670.30091.2949-0.90190.1905207.5299143.615833.5117
90.0076-0.0004-0.00410.0007-0.0010.0019-0.0366-0.05970.0190.01320.00140.0605-0.0287-0.0395-00.6004-0.02040.17581.0967-0.25510.7509186.9199133.917822.6885
100.0656-0.00910.03340.0048-0.00150.03020.0549-0.128-0.00230.00450.042-0.01470.0067-0.10450.01620.7081-0.18170.34361.1008-0.44640.7041194.9613135.072415.8412
110.00130.00520.00070.00240.00060.00040.0141-0.01260.004-0.01510.0006-0.00150.00860.0542-00.7907-0.3239-0.13830.5879-0.06450.59156.9883107.051635.0764
12-0.00020.00350.00050.0035-0.00060.00070.0177-0.0109-0.0146-0.0163-0.0112-0.01950.02230.02501.12510.04680.08620.8856-0.12980.9135154.0977116.775740.4507
130.00330.0058-0.00080.00660.00240.00190.00630.03370.03290.03960.0332-0.0209-0.00920.0218-0.00011.0798-0.12710.02281.0222-0.03450.7797168.2405116.625129.4827
140.0070.0048-0.00880.00380.00420.0048-0.05260.0068-0.0710.066-0.01070.1015-0.0078-0.0464-0.00010.67930.0020.07540.4659-0.12090.5122145.348108.785121.5713
150.0006-0.00010.00030.0031-0.00580.01080.0726-0.0004-0.01350.0750.03690.00680.0129-0.071-00.8953-0.02010.24060.6308-0.01880.5472135.3234104.153838.1568
16-0.00030.0006-0.00170.0001-0.00040.00140.0147-0.04610.00320.01040.0434-0.0032-0.0133-0.010301.2291-0.07570.261.0849-0.0720.9593135.101106.856352.2323
170.0016-0.00180.00030.0047-0.00070.00190.00460.006-0.0110.0059-0.00280.0014-0.03880.0091-01.02910.07060.27640.7814-0.20320.8089131.8641117.06243.4115
18-0.00030.0095-0.00130.01030.00040.0048-0.02040.02460.07540.0487-0.00190.0051-0.03480.05100.77470.00220.19860.5447-0.07040.6909141.0134115.419223.8662
190.00340.00420.00580.00760.00640.011-0.01190.0350.02590.0186-0.0521-0.0289-0.01190.0549-00.5305-0.02970.00490.7413-0.27310.597171.1632125.99434.3738
200.00420.0070.00560.0110.01020.00860.00870.015-0.0070.04810.0008-0.0046-0.03060.084600.589-0.07820.11570.7302-0.24480.6394177.0772125.72861.7946
210.00220.00450.00310.01180.00480.00430.01930.0047-0.0040.03220.02830.0179-0.01320.0201-00.6722-0.07870.16650.6922-0.27460.8433162.0604131.47845.1178
220.0004-0.00160.00040.00080.0014-0.00010.00870.0010.03880.00620.04980.0169-0.00690.010200.7355-0.17040.20890.586-0.19190.7716168.6915134.97395.3994
230.0008-0.00090.00160.0010.00080.00330.0204-0.03160.00530.0165-0.02080.0215-0.0323-0.0169-00.5570.09270.1560.5612-0.15380.6527145.3808129.30481.1764
240.00460.0003-0.00010.00250.00010.001-0.02430.00690.0047-0.023-0.0169-0.01410.0120.0102-00.66570.06810.19880.7065-0.12960.7339154.1803121.0053-10.0341
250.00290.00140.00290.00540.00080.001-0.0204-0.04170.0080.00470.0191-0.0118-0.0062-0.064500.47720.05830.24080.4133-0.11350.5876147.194117.74821.6628
260.00520.0009-0.00070.00410.00390.00790.00070.01930.0056-0.00010.01580.0530.05040.0381-00.5151-0.04830.17420.5287-0.12160.5531154.8399121.70310.1646
270.0016-0.00090.00320.0019-0.00020.0004-0.00870.0025-0.0032-0.0016-0.02040.0127-0.0015-0.035500.56730.19190.18240.5599-0.10750.795137.94134.7647-8.8534
280.0037-0.0010.0067-0.002-0.00220.0111-0.02840.0460.0063-0.00190.00540.0131-0.03820.093800.73230.0489-0.01251.14510.0340.657175.2684117.016-87.7677
290.00130.00190.0004-0.0017-0.00060.00210.0231-0.0009-0.0064-0.03280.0028-0.0021-0.007-0.0256-0.00011.06040.0368-0.16951.20270.01670.6594175.5922112.74-97.882
30-0.00170.0006-0.00020.0008-0.00160.0035-0.00230.0145-0.0008-0.0098-0.02520.0084-0.0105-0.0154-01.18450.014-0.04761.28630.15120.9974167.4966119.2985-90.9691
310.02340.00160.0007-0.0002-0.00010.00350.0050.00140.0071-0.00530.0027-0.0045-0.01520.004601.3678-0.0020.12391.3770.081.2647185.7721126.4224-88.3602
320.0023-0.00050.00250.0057-0.0090.0210.0541-0.0332-0.0042-0.08880.03110.0275-0.0695-0.019400.7401-0.0096-0.02741.0620.17030.6848180.4288118.7564-85.9875
330.0005-0.00090.00020.0008-0.00010.00050.01570.0086-0.02550.01680.02910.01130.0416-0.004101.02060.0963-0.02780.92220.05790.7808170.3963106.6449-85.0391
340.0007-0.00010.00120.0008-0.00150.00240.0063-0.01350.00030.002-0.02060.00220.0088-0.006100.8425-0.00490.1071.0773-0.07120.8814179.1051112.7866-85.3142
350.00210.00050.00440.00460.00270.00190.0048-0.0060.01510.0049-0.0053-0.0051-0.0006-0.00740.00011.05470.1309-0.14681.10220.1910.9795167.2774131.6362-73.3094
360.0039-0.00440.00170.0034-0.0017-0.0002-0.00730.0041-0.02350.01360.00210.017-0.02850.0226-00.8209-0.0093-0.02860.9928-0.05421.0872219.3611143.1066-24.0175
370.01770.01630.01590.02060.00270.03310.04820.06920.1178-0.0677-0.0168-0.0942-0.04640.012700.5901-0.12830.24630.8321-0.08010.7216241.3008138.3318-30.8584
380.0023-0.0009-0.00150.00440.00520.01690.00050.01040.0064-0.0384-0.00420.03170.01160.0197-00.65560.12480.24970.8648-0.18140.5611231.2104127.3107-42.5221
390.0034-0.0002-0.00120.0016-0.00140.00090.06090.0203-0.0179-0.00450.02820.0316-0.05960.021500.34720.15510.06830.44970.06710.4489141.4182123.5818-30.035
400.0032-0.0017-0.00250.00120.0020.0020.01970.01060.0081-0.00670.0054-0.0139-0.0242-0.0019-00.39120.07280.19280.53150.03350.5674140.609133.1868-31.2012
410.0014-0.0014-0.00190.0027-0.00160.0024-0.00280.0062-0.005-0.0124-0.02010.01380.0057-0.0197-00.35680.10320.12060.45130.16470.4775128.0175126.82-27.0861
420.002-0.00370.00020.00430.00010.0017-0.00770.0220.0223-0.001-0.01660.0522-0.02850.0053-00.56830.08660.07640.58150.08190.8353133.2316133.3818-33.2768
430.0024-0.0042-0.0020.00470.00390.00180.0217-0.02250.0374-0.00110.075-0.01980.0504-0.01230.00010.57210.14850.18050.5876-0.09920.6941146.9655141.1246-16.4595
440.0007-0.0006-0.00290.00190.0022-0.0006-0.0263-0.03080.05650.00660.0143-0.0148-0.01150.007-00.68140.13360.15520.49460.08890.7835144.6936130.3869-18.1264
450.00040.00030.00020.00130.00090.00130.00860.0095-0.00330.0123-0.01920.01350.0409-0.0152-00.48460.12160.01110.40570.01240.4674135.1647109.8735-23.7782
460.0051-0.0031-0.00640.00070.00280.00510.0152-0.0730.02450.04810.0062-0.0025-0.01620.0115-0.00010.33860.08590.1590.56590.03040.4553131.2533118.2301-12.6296
470.0025-0.0012-0.00020.0014-0.00240.00270.01430.01450.0022-0.0193-0.00820.0574-0.0087-0.004-00.54680.02130.13970.63290.05410.6599127.2386119.4462-17.1337
480.0064-0.00760.00370.00450.00050.00740.0214-0.00150.0354-0.01240.0003-0.01160.0015-0.0298-01.0424-0.30070.16540.9034-0.08891.2324239.4065166.8813-4.6045
490.00030.0014-0.00060.005-0.00250.00310.02660.00870.0139-0.00720.0056-0.0111-0.0066-0.0022-01.1273-0.24250.01351.1389-0.12821.2626252.0654165.7489-7.6914
500.0040.0011-0.00010.00350.00240.0022-0.0224-0.0155-0.00280.0102-0.0082-0.01-0.0083-0.0044-01.1325-0.09260.21761.2543-0.17121.3303251.5943155.9376-9.8388
510.0034-0.0014-0.0060.0071-0.0028-0.0001-0.05080.00290.03040.0603-0.0748-0.0172-0.00460.011500.9304-0.43770.03161.0202-0.13311.0307244.0942164.461-12.9604
520.0010.00050.00030.0011-0.0013-0.00080.00920.04110.00720.00720.02020.0053-0.00260.0198-00.6853-0.25880.06770.7743-0.14061.0965238.3019164.2708-9.9806
530.00790.00130.00670.0110.01530.01430.0294-0.01040.15740.0413-0.0054-0.03030.0879-0.0017-0.00010.6913-0.17940.17240.9828-0.31240.8832228.996154.8813-10.0825
540.00660.0001-0.002200.00070.00350.0383-0.00080.0559-0.01670.032-0.00940.02670.0016-0.00010.7465-0.1410.07750.8513-0.13660.7988223.7327123.2893-7.2927
550.00090.001-0.00120.00090.00080.00120.0245-0.0174-0.0114-0.00650.01990.0038-0.00220.008401.5285-0.15590.06421.5429-0.1621.5571231.9424161.70228.5358
560.0032-0.00020.00230.00060.00130.00040.02050.03580.00150.01810.01940.0023-0.0319-0.0464-00.9997-0.0835-0.00981.1361-0.18121.0698220.6492164.52924.5174
570.01410.0051-0.0420.01390.01310.0034-0.0282-0.05730.0738-0.05930.0253-0.01830.08470.0325-0.01860.7553-0.3350.34350.7173-0.50540.5702225.3578151.667819.5696
580.00130.0009-0.00330.00030.00340.00080.0194-0.01210.0040.00980.03430.0121-0.0158-0.0306-0.00021.42450.00990.17821.4639-0.27511.332221.2995165.811635.7927
590.01750.00640.0030.0030.00210.0014-0.01420.0058-0.0092-0.006-0.04010.01790.00720.0070.00011.3926-0.0113-0.1221.3496-0.23161.4065230.466158.961431.7663
600.0075-0.00270.00360.00260.0020.0035-0.0170.00070.02560.01640.03790.00190.0002-0.030400.6277-0.00810.25120.81930.10960.7038214.6398118.4442-68.9904
610.0148-0.0137-0.00430.0145-0.00710.0066-0.0087-0.05360.0021-0.00670.0522-0.0545-0.01480.0421-00.48520.10420.16820.76120.11310.5463217.4848120.8117-63.7197
620.00510.00220.00390.00130.00050.0018-0.02270.00870.00380.0021-0.0451-0.0005-0.0031-0.05720.00010.6392-0.11910.00140.81590.17940.6907212.9609129.7266-69.2394
630.0018-0.0019-0.00220.00490.00460.00210.00690.0170.001300.0092-0.00180.00270.009500.7230.01180.14860.77160.01340.6737193.9928112.987-61.9511
640.0023-0.0001-0.00040.00120.00110.0005-0.01410.0016-0.01550.0111-0.0175-0.01040.00180.010100.61450.14270.05520.6011-0.14030.7459195.9928107.8078-50.0246
650.00140.00060.00070.00130.0003-0.0002-0.01620.02060.00510.0045-0.0027-0.0018-0.00080.009300.38970.06980.06080.48840.08410.5618145.9455100.2321-26.7385
66-0.00070.00030.00150.0002-0.00130.0007-0.0053-0.0329-0.0079-0.02250.00160.0041-0.00920.028-00.68950.06390.06920.6988-0.06810.7141154.39891.0887-14.3965
670.0021-0.00140.00110.00130.0010.00150.0159-0.00160.0125-0.00890.00630.012-0.01180.007600.45590.1243-0.06810.3858-0.00210.3092161.896779.10351.2785
680.0193-0.0066-0.00870.0256-0.00240.0153-0.0113-0.0047-0.06750.1007-0.0019-0.16650.13190.0233-00.41880.1285-0.1180.6327-0.01170.7329175.427379.872910.3853
690.00280.00130.00580.00130.00430.01320.0037-0.00880.0035-0.00190.00630.00340.0024-0.0005-01.04590.0089-0.05771.07590.06181.0503169.8283.925434.9843
700.0023-0.0005-0.00050.0011-0.0004-0.0008-0.0155-0.0163-0.02790.01960.0002-0.00640.05620.0205-01.0292-0.15280.12321.1505-0.11181.0701275.1591116.0539-8.3652
710.0069-0.00330.0030.0025-0.00040.0029-0.03390.00380.0384-0.0294-0.04120.0331-0.07350.0024-00.3527-0.0009-0.00431.0368-0.11050.8873273.7622123.3104-2.9231
720.00230.00070.0007-0.0004-0.0014-00.0355-0.00440.0090.00570.0233-0.02130.00840.006800.7539-0.0398-0.1211.2393-0.07381.1135282.9754119.4205-0.4354
730.0009-0.00080.00110.0057-0.00050.0013-0.0114-0.0035-0.00470.0094-0.0084-0.0031-0.0109-0.0122-01.035-0.1202-0.08721.16260.0151.0389274.9925113.96677.4363
740.0023-0.00060.00180.0004-0.00260.0031-0.0240.00370.0291-0.0149-0.0065-0.03050.00260.0049-00.8450.1241-0.11861.17210.04660.9418263.8977102.51689.9519
750.0005-0.0007-0.00090.0008-0.00020.00190.0167-0.0024-0.00690.00550.0195-0.008-0.0016-0.0106-00.9630.03110.01371.2272-0.08791.0005251.2051100.358414.5458
760.00130.00220.00150.0003-0.00020.0018-0.0322-0.0132-0.01480.01770.0031-0.00090.02150.03300.70850.02460.04471.0672-0.01440.6687242.1146104.46343.1017
770.00410.0021-00.00250.00090.00080.0008-0.0055-0.0070.00380.01650.00490.0004-0.003301.10470.04940.01731.1769-0.10851.0794221.3534118.666633.624
780.0088-0.0068-0.00180.00560.0020.0004-0.0034-0.00140.00630.00320.00370.00170.00050.0007-0.00011.3522-0.0474-0.05541.4104-0.09391.359229.8987123.582940.9977
790.0016-0.00250.00080.0338-0.01350.00650.00020.00570.00160.00120.0062-0.0031-0.0065-0.00501.0975-0.0639-0.00891.3053-0.12331.0917237.1935120.290834.9509
800.0154-0.00280.00390.0017-0.00120.0010.00590.0029-0.00240.01650.0087-0.02180.0111-0.001601.0503-0.05470.09731.0296-0.03920.9578226.3199124.845629.1982
810.0009-0.0008-0.00060.00180.0010.0005-0.01140.00780.0054-0.0002-0.0029-0.00610.00140.001100.82220.01830.01281.052-0.07340.7549217.7324127.10926.8722
820.0013-0.0021-0.00080.00250.00280.0077-0.0115-0.01680.01130.0287-0.0347-0.02850.04220.0441-00.8767-0.15810.11161.0168-0.32140.7783219.4428132.688621.7073
830.00090.0013-0.00210.0015-00.00050.00150.03010.054-0.0529-0.0229-0.03090.00380.0042-00.8638-0.09480.09111.106-0.22951.0386217.1776143.765116.3715
840.0011-0.0003-0.0010.001-0.00220.00270.01220.0156-0.0096-0.04230.0054-0.0089-0.02670.038800.91180.0645-0.06851.06660.15250.8255142.9387111.0634-73.5807
850.00160.00280.00090.0035-0.00390.00820.01180.04550.0189-0.03620.05790.025-0.04850.0015-00.58710.0687-0.17380.88270.12880.513143.0949106.2279-66.0161
860.00440.00940.00460.01030.00920.01650.051-0.0372-0.01620.01530.08770.04540.0175-0.0529-00.74430.0875-0.10090.9733-0.07170.7923148.1272101.5944-57.2477
870.00150.00040.00240.00060.00120.0031-0.01960.0123-0.0205-0.00880.00870.01350.0471-0.0437-00.8476-0.0687-0.20580.99920.07080.8702132.921898.2184-63.2281
880.0055-0.0033-0.00790.00610.00060.00490.0396-0.00310.07460.02690.09120.0260.0501-0.006400.6737-0.01770.21760.63960.01230.8191117.44677.900512.2148
890.0029-0.00150.00010.00280.00120.00050.01040.0090.00170.00520.0158-0.00820.011-0.0087-00.8756-0.07410.24550.8981-0.16490.9695114.951186.454326.2062
900.00270.0002-0.00050.00150.0030.0024-0.01740.02790.0029-0.04270.01240.0126-0.0076-0.025-00.60220.07620.23930.64830.04880.8237103.885882.64829.3257
910.00360.0009-0.00210.0044-0.00470.006-0.0007-0.0571-0.0138-0.0106-0.06580.03910.00450.003-00.7443-0.21040.3140.69560.1040.7757102.3376.540816.6515
920.00410.00130.0034-0.00210.00040.00160.0056-0.05760.01310.01010.01950.0206-0.0093-0.028600.4366-0.097-0.05250.53130.17420.5468120.591586.1929-33.3669
930.009-0.0034-0.00010.0055-0.00090.00170.0708-0.03230.04590.01320.0176-0.013-0.05180.0273-0.00010.6068-0.1526-0.03890.76690.07660.6368126.32584.1262-36.6808
940.00270.0026-0.00010.0066-0.00970.0056-0.0098-0.0362-0.0181-0.0340.01270.00820.07830.0034-00.5897-0.06330.04280.64140.12570.658132.348591.1977-28.3048
950.01730.00190.00770.00870.00490.0036-0.02540.002-0.0299-0.0309-0.03020.0202-0.053-0.0054-00.6089-0.1374-0.07460.7610.20440.6428118.076981.7562-37.8526
960.0003-0.0016-0.00060.0001-0.00150.0030.01550.00640.0005-0.01380.03170.0188-0.00810.017200.9503-0.14770.13220.95530.06840.768136.8687.4705-44.4384
970.009-0.01220.00320.0219-0.00370.0007-0.00840.0007-0.0026-0.0032-0.01380.0006-0.0015-0.00530.00010.7774-0.0078-0.0240.83190.05560.8675153.21480.7446-41.3924
980.0083-0.003-0.00010.0053-0.00030.01670.001-0.0018-0.00040.00190.00010.00140.00220.000302.2132-0.0074-0.00092.2094-0.05262.1897187.6675140.7726-58.0392
99-0.0002-0.00160.00040.0020.00040.0036-0.01870.00340.045-0.0065-0.01940.0092-0.0296-0.023900.89250.1250.15490.92330.13080.8494178.1662133.5057-73.3909
1000.0010.00020.0020.00070.00040.00390.0099-0.00730.0048-0.00350.0186-0.0419-0.02040.00500.79320.07630.09850.95660.02760.6797184.3314131.0314-63.2776
1010.0041-0.0033-0.00780.0037-0.00050.00710.08460.04060.0018-0.05780.0981-0.02870.01990.05190.00010.6780.10830.03420.87880.17490.5292184.0822124.8997-69.8827
1020.0018-0.00060.00140.0028-0.00250.0002-0.0433-0.0284-0.0431-0.03120.02520.01390.0245-0.0016-0.00010.86620.0074-0.17211.1092-0.04151.0023254.2066114.656327.8498
103-0.0005-0.001-0.0006-0.0005-0.00090.00040.0010.0029-0.00670.0177-0.004-0.01350.007-0.002701.63640.096-0.04861.90530.07831.4852253.8125102.076342.8179
1040.01680.01130.00450.00730.00250.0010.00520.00090.00180.00090.0008-0.00190.0085-0.00970.00011.8897-0.040.00471.91020.08711.9512252.764190.923540.4467
1050.00030.00060.0003-0.0009-0.00130.003-0.00930.0081-0.0286-0.011-0.00140.00660.0039-0.0182-01.0925-0.0112-0.18121.44520.07791.1522251.3984102.241933.4507
1060.0042-0.0003-0.0041-0.0015-0.0020.0074-0.0324-0.0047-0.02430.00270.0002-0.04640.0220.0389-00.64730.0018-0.16141.01340.10320.5687247.727998.18825.1246
1070.00750.01350.00620.0277-0.00810.00260.0296-0.04520.03-0.00850.0191-0.01160.03520.0181-00.9027-0.15180.01840.50070.10640.7202114.12442.6467-13.416
1080.00060.00300.0042-0.00310.00180.0352-0.1133-0.0320.0448-0.00910.0761-0.00510.02600.682-0.1427-0.02460.43280.16820.707199.208644.0016-27.2371
1090.0007-0.0010.00150.0109-0.00450.00450.0024-0.0015-0.00340.01040.00210.0020.02970.010700.6315-0.0701-0.13280.62320.05940.7027107.858753.5058-14.3397
1100.00070.0028-0.00450.0025-0.00220.0087-0.00270.02670.017-0.0435-0.07360.0214-0.0173-0.0022-00.8299-0.186-0.05960.84380.28530.8237100.206751.363-33.5203
1110.0046-0.00260.00410.0045-0.00250.007-0.0025-0.0064-0.00670.01060.0078-0.00660.00960.0103-00.8393-0.0737-0.0031.0042-0.11040.885253.485125.64792.2409
1120.00360.0004-0.00250.0020.00090.00520.0181-0.03580.0001-0.00330.0166-0.0057-0.00250.0216-00.9206-0.2213-0.03761.1188-0.26211.0645253.2619132.70487.2131
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 1401:1544)A0
4X-RAY DIFFRACTION4chain 'B' and (resseq 6:63)B6 - 63
5X-RAY DIFFRACTION5chain 'B' and (resseq 64:104)B64 - 104
6X-RAY DIFFRACTION6chain 'B' and (resseq 105:148)B105 - 148
7X-RAY DIFFRACTION7chain 'B' and (resseq 149:241)B149 - 241
8X-RAY DIFFRACTION8chain 'C' and (resseq 2:112)C2 - 112
9X-RAY DIFFRACTION9chain 'C' and (resseq 113:143)C113 - 143
10X-RAY DIFFRACTION10chain 'C' and (resseq 144:208)C144 - 208
11X-RAY DIFFRACTION11chain 'D' and (resseq 2:14)D2 - 14
12X-RAY DIFFRACTION12chain 'D' and (resseq 15:34)D15 - 34
13X-RAY DIFFRACTION13chain 'D' and (resseq 35:52)D35 - 52
14X-RAY DIFFRACTION14chain 'D' and (resseq 53:99)D53 - 99
15X-RAY DIFFRACTION15chain 'D' and (resseq 100:148)D100 - 148
16X-RAY DIFFRACTION16chain 'D' and (resseq 149:164)D149 - 164
17X-RAY DIFFRACTION17chain 'D' and (resseq 165:181)D165 - 181
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)D182 - 209
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:20)E5 - 20
20X-RAY DIFFRACTION20chain 'E' and (resseq 21:35)E21 - 35
21X-RAY DIFFRACTION21chain 'E' and (resseq 36:50)E36 - 50
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:64)E51 - 64
23X-RAY DIFFRACTION23chain 'E' and (resseq 65:79)E65 - 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 141:155)E141 - 155
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:15)F1 - 15
29X-RAY DIFFRACTION29chain 'F' and (resseq 16:32)F16 - 32
30X-RAY DIFFRACTION30chain 'F' and (resseq 33:42)F33 - 42
31X-RAY DIFFRACTION31chain 'F' and (resseq 43:47)F43 - 47
32X-RAY DIFFRACTION32chain 'F' and (resseq 48:68)F48 - 68
33X-RAY DIFFRACTION33chain 'F' and (resseq 69:81)F69 - 81
34X-RAY DIFFRACTION34chain 'F' and (resseq 82:92)F82 - 92
35X-RAY DIFFRACTION35chain 'F' and (resseq 93:101)F93 - 101
36X-RAY DIFFRACTION36chain 'G' and (resseq 2:11)G2 - 11
37X-RAY DIFFRACTION37chain 'G' and (resseq 12:128)G12 - 128
38X-RAY DIFFRACTION38chain 'G' and (resseq 129:156)G129 - 156
39X-RAY DIFFRACTION39chain 'H' and (resseq 1:18)H1 - 18
40X-RAY DIFFRACTION40chain 'H' and (resseq 19:29)H19 - 29
41X-RAY DIFFRACTION41chain 'H' and (resseq 30:41)H30 - 41
42X-RAY DIFFRACTION42chain 'H' and (resseq 42:62)H42 - 62
43X-RAY DIFFRACTION43chain 'H' and (resseq 63:72)H63 - 72
44X-RAY DIFFRACTION44chain 'H' and (resseq 73:85)H73 - 85
45X-RAY DIFFRACTION45chain 'H' and (resseq 86:95)H86 - 95
46X-RAY DIFFRACTION46chain 'H' and (resseq 96:114)H96 - 114
47X-RAY DIFFRACTION47chain 'H' and (resseq 115:138)H115 - 138
48X-RAY DIFFRACTION48chain 'I' and (resseq 2:21)I2 - 21
49X-RAY DIFFRACTION49chain 'I' and (resseq 22:32)I22 - 32
50X-RAY DIFFRACTION50chain 'I' and (resseq 33:40)I33 - 40
51X-RAY DIFFRACTION51chain 'I' and (resseq 41:69)I41 - 69
52X-RAY DIFFRACTION52chain 'I' and (resseq 70:88)I70 - 88
53X-RAY DIFFRACTION53chain 'I' and (resseq 89:119)I89 - 119
54X-RAY DIFFRACTION54chain 'I' and (resseq 120:128)I120 - 128
55X-RAY DIFFRACTION55chain 'J' and (resseq 3:10)J3 - 10
56X-RAY DIFFRACTION56chain 'J' and (resseq 11:28)J11 - 28
57X-RAY DIFFRACTION57chain 'J' and (resseq 29:80)J29 - 80
58X-RAY DIFFRACTION58chain 'J' and (resseq 81:93)J81 - 93
59X-RAY DIFFRACTION59chain 'J' and (resseq 94:101)J94 - 101
60X-RAY DIFFRACTION60chain 'K' and (resseq 11:34)K11 - 34
61X-RAY DIFFRACTION61chain 'K' and (resseq 35:99)K35 - 99
62X-RAY DIFFRACTION62chain 'K' and (resseq 100:110)K100 - 110
63X-RAY DIFFRACTION63chain 'K' and (resseq 111:120)K111 - 120
64X-RAY DIFFRACTION64chain 'K' and (resseq 121:127)K121 - 127
65X-RAY DIFFRACTION65chain 'L' and (resseq 5:12)L5 - 12
66X-RAY DIFFRACTION66chain 'L' and (resseq 13:22)L13 - 22
67X-RAY DIFFRACTION67chain 'L' and (resseq 23:31)L23 - 31
68X-RAY DIFFRACTION68chain 'L' and (resseq 32:122)L32 - 122
69X-RAY DIFFRACTION69chain 'L' and (resseq 123:129)L123 - 129
70X-RAY DIFFRACTION70chain 'M' and (resseq 2:14)M2 - 14
71X-RAY DIFFRACTION71chain 'M' and (resseq 15:49)M15 - 49
72X-RAY DIFFRACTION72chain 'M' and (resseq 50:61)M50 - 61
73X-RAY DIFFRACTION73chain 'M' and (resseq 62:66)M62 - 66
74X-RAY DIFFRACTION74chain 'M' and (resseq 67:83)M67 - 83
75X-RAY DIFFRACTION75chain 'M' and (resseq 84:93)M84 - 93
76X-RAY DIFFRACTION76chain 'M' and (resseq 94:119)M94 - 119
77X-RAY DIFFRACTION77chain 'N' and (resseq 2:9)N2 - 9
78X-RAY DIFFRACTION78chain 'N' and (resseq 10:14)N10 - 14
79X-RAY DIFFRACTION79chain 'N' and (resseq 15:19)N15 - 19
80X-RAY DIFFRACTION80chain 'N' and (resseq 20:24)N20 - 24
81X-RAY DIFFRACTION81chain 'N' and (resseq 25:29)N25 - 29
82X-RAY DIFFRACTION82chain 'N' and (resseq 30:50)N30 - 50
83X-RAY DIFFRACTION83chain 'N' and (resseq 51:61)N51 - 61
84X-RAY DIFFRACTION84chain 'O' and (resseq 2:15)O2 - 15
85X-RAY DIFFRACTION85chain 'O' and (resseq 16:44)O16 - 44
86X-RAY DIFFRACTION86chain 'O' and (resseq 45:73)O45 - 73
87X-RAY DIFFRACTION87chain 'O' and (resseq 74:89)O74 - 89
88X-RAY DIFFRACTION88chain 'P' and (resseq 1:39)P1 - 39
89X-RAY DIFFRACTION89chain 'P' and (resseq 40:48)P40 - 48
90X-RAY DIFFRACTION90chain 'P' and (resseq 49:61)P49 - 61
91X-RAY DIFFRACTION91chain 'P' and (resseq 62:84)P62 - 84
92X-RAY DIFFRACTION92chain 'Q' and (resseq 2:12)Q2 - 12
93X-RAY DIFFRACTION93chain 'Q' and (resseq 13:28)Q13 - 28
94X-RAY DIFFRACTION94chain 'Q' and (resseq 29:45)Q29 - 45
95X-RAY DIFFRACTION95chain 'Q' and (resseq 46:81)Q46 - 81
96X-RAY DIFFRACTION96chain 'Q' and (resseq 82:97)Q82 - 97
97X-RAY DIFFRACTION97chain 'Q' and (resseq 98:102)Q98 - 102
98X-RAY DIFFRACTION98chain 'R' and (resseq 16:20)R16 - 20
99X-RAY DIFFRACTION99chain 'R' and (resseq 21:43)R21 - 43
100X-RAY DIFFRACTION100chain 'R' and (resseq 44:59)R44 - 59
101X-RAY DIFFRACTION101chain 'R' and (resseq 60:88)R60 - 88
102X-RAY DIFFRACTION102chain 'S' and (resseq 2:12)S2 - 12
103X-RAY DIFFRACTION103chain 'S' and (resseq 13:25)S13 - 25
104X-RAY DIFFRACTION104chain 'S' and (resseq 26:30)S26 - 30
105X-RAY DIFFRACTION105chain 'S' and (resseq 31:47)S31 - 47
106X-RAY DIFFRACTION106chain 'S' and (resseq 48:82)S48 - 82
107X-RAY DIFFRACTION107chain 'T' and (resseq 8:45)T8 - 45
108X-RAY DIFFRACTION108chain 'T' and (resseq 46:68)T46 - 68
109X-RAY DIFFRACTION109chain 'T' and (resseq 69:75)T69 - 75
110X-RAY DIFFRACTION110chain 'T' and (resseq 76:106)T76 - 106
111X-RAY DIFFRACTION111chain 'U' and (resseq 2:8)U2 - 8
112X-RAY DIFFRACTION112chain 'U' and (resseq 9:26)U9 - 26

+
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