[English] 日本語
Yorodumi
- PDB-8wrc: Time-Resolved Ambient Temperature Kineto-Crystallographic Structu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wrc
TitleTime-Resolved Ambient Temperature Kineto-Crystallographic Structure of Initiation Factor in Complex with Ribosome
Components
  • (30S ribosomal protein ...) x 19
  • 16S rRNA
  • Small ribosomal subunit protein uS12
  • Translation initiation factor IF-1
KeywordsRIBOSOME / sfx / kineto-crystallography / structural dynamics
Function / homology
Function and homology information


translation initiation factor activity / ribosome binding / 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 ...translation initiation factor activity / ribosome binding / 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
Translation initiation factor IF-1 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S3, bacterial-type / Ribosomal protein S14/S29 ...Translation initiation factor IF-1 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S3, bacterial-type / Ribosomal protein S14/S29 / 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 / K Homology domain / K homology RNA-binding domain / 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. / 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 / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / : / K homology domain superfamily, prokaryotic type / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / K homology domain-like, alpha/beta / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S10p/S20e
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS17 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS17 / 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 / Small ribosomal subunit protein uS5 / Translation initiation factor IF-1 / 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 HB8 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsDeMirci, H. / Yapici, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: To Be Published
Title: Time-Resolved Kineto-Crystallography Reveals the First Initiation Factor Ribosome Binding Dynamics
Authors: Yapici, I. / DeMirci, H.
History
DepositionOct 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

-
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: Small ribosomal subunit protein uS12
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
W: Translation initiation factor IF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)798,354278
Polymers792,05022
Non-polymers6,304256
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)402.600, 402.600, 175.900
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 rRNA


Mass: 494168.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: GenBank: NR_037066

-
30S ribosomal protein ... , 19 types, 19 molecules BCDEFGHIJKMNOPQRSTU

#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 HB8 (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 HB8 (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 HB8 (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 genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: rpsE, TTHA1675 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ5
#6: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: rpsF, TTHA0245 / Production host: Thermus thermophilus HB8 (bacteria) / 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 HB8 (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 HB8 (bacteria) / Strain: HB8 / References: UniProt: P0DOY9
#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 HB8 (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 HB8 (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 HB8 (bacteria) / Strain: HB8 / References: UniProt: P80376
#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 HB8 (bacteria) / Strain: HB8 / 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 HB8 (bacteria) / Strain: HB8 / References: UniProt: P0DOY6
#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 HB8 (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 HB8 (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 HB8 (bacteria) / Strain: HB8 / References: UniProt: P24321
#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 HB8 (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 HB8 (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 HB8 (bacteria) / Strain: HB8 / 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 HB8 (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

-
Protein , 2 types, 2 molecules LW

#12: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 14966.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: A0A3P4AU90, UniProt: Q5SHN3
#22: Protein Translation initiation factor IF-1


Mass: 8116.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: infA / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHR1

-
Non-polymers , 3 types, 505 molecules

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


Mass: 24.305 Da / Num. of mol.: 254 / 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


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPD

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.29 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29 Å / Relative weight: 1
ReflectionResolution: 3.59→51.91 Å / Num. obs: 176058 / % possible obs: 98.22 % / Redundancy: 1076 % / CC1/2: 0.48 / R split: 1.2 / Net I/σ(I): 3.1
Reflection shellResolution: 3.59→3.73 Å / Num. unique obs: 19504 / CC1/2: 0.032
Serial crystallography sample deliveryMethod: injection

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.59→51.91 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2819 523 0.32 %
Rwork0.2334 --
obs0.2336 164359 98.22 %
Refinement stepCycle: LAST / Resolution: 3.59→51.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19658 32486 505 0 52649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256733
X-RAY DIFFRACTIONf_angle_d0.58584115
X-RAY DIFFRACTIONf_dihedral_angle_d17.49526333
X-RAY DIFFRACTIONf_chiral_restr0.03510496
X-RAY DIFFRACTIONf_plane_restr0.0044987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.59-4.520.38151340.327241398X-RAY DIFFRACTION100
4.52-5.70.2761310.255341596X-RAY DIFFRACTION100
5.7-51.910.2331370.165442571X-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)
10.8529-0.0653-0.00510.4378-0.15970.54290.1395-0.2807-0.25140.1057-0.1234-0.1898-0.04220.2631-0.00470.78-0.2507-0.0680.91770.22111.6052118.148344.6231.012
20.67970.2892-0.05292.83760.92310.54880.2919-0.44960.52821.7495-0.1230.59820.0813-0.2803-0.18672.54370.0790.92611.28230.0012.254272.1461423.607753.3826
30.8929-1.27570.51572.4428-0.92360.080.29340.20970.72060.2339-0.3688-0.9942-0.27260.45580.08711.2682-0.2752-0.0851.3530.25051.9131.0059365.781217.6021
42.0007-3.7733-3.23883.811-3.98432.0006-0.5678-7.0957-8.536913.50712.2622-0.75622.5433-0.5805-1.77515.4723-0.0976-0.37431.95180.65283.262393.6135408.257511.4034
52.7377-2.5489-3.42862.37193.18124.39540.96061.28383.5322-0.58150.1955-0.11730.0728-1.2718-1.24361.01940.4453-0.39881.83830.28232.102743.926357.20469.4084
64.49551.3863-5.90867.3170.1698.7135-0.54830.6329-0.6559-0.14660.9922.19691.4923-2.4286-0.4990.7569-0.0213-0.06261.63670.49022.129845.8346351.132516.296
76.13360.79360.75814.34254.27969.01160.45461.02521.1637-1.6986-1.00860.6976-2.2283-0.51140.69171.24030.63010.17271.95230.96642.316339.3062367.971525.015
86.9503-3.49772.85475.0983-0.052.23690.30080.23120.47841.33860.80711.0824-0.8376-0.7015-0.9351.60990.16821.05771.14320.50222.287644.4615375.018937.0562
94.29682.75371.58424.65881.45790.64520.4458-0.40682.09530.85230.51541.0884-1.0751-1.1005-0.81452.32880.41241.62162.21050.44243.401139.3421391.107639.1938
101.0597-0.51670.09691.34021.96354.0120.18710.6361.28890.0154-0.30050.4861-0.7775-1.56530.1740.56560.03940.36851.59580.67362.765945.4559361.184825.4236
110.07090.243-0.13460.8697-0.48590.25120.645-0.56750.38640.3278-0.15311.3133-0.0466-0.3767-0.52330.69060.17340.24893.99110.04173.464827.1013363.990620.713
122.16660.3149-0.16810.0256-0.01420.00970.3086-1.11961.11711.2597-0.69980.51521.02770.1069-0.34735.4027-0.40111.42671.9458-0.18671.713761.9523406.085578.3897
133.05041.1238-0.23373.9902-0.85220.79420.5657-0.23290.04772.511-0.2136-0.33531.11310.10710.15424.51830.04510.90471.09030.44941.648570.1848391.012362.1558
146.36015.6103-1.67288.5659-4.8823.66181.3834-1.00620.63461.46820.30650.7233-0.97760.3844-1.6092.04440.19980.22962.4782-0.15131.876890.5769354.520981.6544
158.8467-5.08170.27853.33581.58119.1445-0.144-1.80291.79222.00271.09390.6732-1.3558-0.7431-0.81661.632-0.28890.21571.5179-0.21191.417788.5116360.979269.2328
160.6421-1.05532.09913.5008-1.41539.1366-0.0843-0.406-0.14460.18920.27060.59630.84810.4061-0.06370.6192-0.18980.08521.7550.54621.444697.9941336.682774.7732
174.5899-0.12461.25246.61234.72475.44670.5689-1.3533-0.64192.6566-0.08121.28870.4288-0.7946-0.33691.629-0.35060.08472.68190.69240.712291.6848332.550691.3846
185.63542.5614-3.25917.9036-4.88983.9184-1.0387-0.12430.4024-1.30130.31841.11821.3582-1.43340.42251.3463-0.4782-0.64841.48820.34870.981887.8149340.215667.1032
194.13793.6631-2.11094.8953-1.76093.64180.21-1.4936-0.15090.4104-0.07550.6389-0.3254-0.47390.0691.7851-0.0811.25551.41870.11.004775.2986363.216352.2082
206.06926.0301-5.51766.9094-7.31228.8204-0.5761-0.54360.10540.6737-0.4941-0.52770.1797-0.31.36612.34340.02570.65640.8514-0.02811.810179.2786384.982141.2726
217.16882.6811-1.35144.0599-0.58345.91670.1241-0.5567-0.09320.62550.10551.3592-0.57110.2205-0.30090.92120.18960.63481.06970.21311.463672.4499363.18548.5391
226.00524.38-1.84654.1910.53188.29260.2622-0.03430.23241.33830.12051.3404-0.5836-0.441-0.50921.37030.55550.63121.7271.12181.634568.6822368.910249.5039
232.13690.18923.04951.5573-1.56048.8828-0.333-0.44760.4186-0.21711.09251.85840.9843-1.4657-0.85730.88450.00540.16520.73990.0151.660872.6597346.212444.4892
247.46487.4323-4.47717.3992-4.3727.3940.67010.23050.6198-0.9831-0.041-2.7653-0.44260.3471-0.44130.7519-0.2640.0430.62960.11791.898181.8607353.46532.8203
252.64861.21690.29491.6781.23932.3309-0.08810.10920.17580.1524-0.2762-0.08251.2497-0.95520.37590.835-0.35780.42020.93530.7291.925285.2395346.782444.9664
264.1316-0.58270.77194.0652-5.00257.37410.65110.21281.2430.4512-0.2111-0.9551-1.22460.0431-0.31071.0350.21330.46060.54520.23480.9581.2988354.500643.5309
278.58924.74775.06653.52043.97534.512-1.1426-1.1365-0.168-0.77-0.26371.70040.2958-0.34891.34810.9387-0.05290.10410.87060.14941.775367.9047337.571135.106
287.30983.2168-4.75563.5383-4.52315.8918-0.29611.2407-0.1985-0.9773-0.1563-0.3442-0.3413-0.08260.38111.4638-0.18230.1151.50780.00340.809586.3225374.768-50.7198
297.337-3.2953-0.93526.87466.57217.2250.39040.43991.1405-1.36390.4834-0.4093-0.5482-0.201-0.75221.0579-0.17820.06851.01450.52550.938585.403375.6691-44.1416
306.51-4.1321-4.71533.08333.14196.5263-0.7322-0.5923-3.5423-0.2558-0.24491.53331.6730.74890.97721.85580.2054-1.02240.89080.2493.014169.6914366.5749-30.498
310.4227-0.42990.90149.83062.20452.9703-1.9046-1.3393-3.83611.19220.2765.06291.6057-0.92190.94031.480.15060.72931.29080.45832.49257.5609418.162220.3907
321.0478-2.4073-2.13195.75715.36385.27950.3082-0.7371-1.26330.15940.5624.6063-0.5855-2.4813-0.89411.14620.16260.08921.37260.41243.857948.2476439.869719.0593
333.5999-1.19673.15971.28460.24.5146-0.59620.74481.3542-0.6902-0.5166-0.3236-0.23340.19771.04571.49650.04880.86221.2290.39013.912457.4437445.827721.0971
346.8537-3.99866.10162.3337-3.56085.4278-0.5902-0.25971.215-1.0428-0.9491.008-0.11180.2681.4811.71710.94450.70171.55490.81423.857853.4454454.78126.62
359.1365-6.1425-7.29844.54195.69747.22773.24963.54470.145-3.8669-3.5146-0.3892-1.0797-1.05210.42692.31810.568-0.20261.5930.04771.728963.735433.93665.995
360.284-1.0306-1.40863.81215.14786.9891-0.12220.5072-0.27620.2240.6499-0.26460.91040.9032-0.62112.0995-0.2093-0.0381.11230.19981.383175.731420.41974.8694
371.1890.3895-0.95951.97972.13663.99520.5361-0.466-0.4644-0.78840.40480.5230.5317-0.7815-0.91681.34250.6312-0.72051.3426-0.15122.709964.733435.709412.7311
383.2932-1.7831-1.37721.65342.00533.88791.09150.3746-0.0162-1.6522-0.57510.1154-2.0352-0.4927-0.36831.78540.271-0.38810.58440.40842.787266.006451.514813.0152
394.4558-2.53564.73854.1331-0.94616.16650.45041.51840.067-2.1566-0.0247-1.02571.3984-0.0755-0.44791.99570.2792-0.06631.9578-0.25081.576571.5899438.66853.0547
405.75254.3049-0.58414.0762-2.27754.0118-0.9096-2.9161-3.1393-1.1184-1.04042.17362.51821.81231.88863.1131-0.05670.61422.31740.40632.838474.8339420.2943-1.154
414.4322-4.02852.75899.52310.1362.91040.2541.28971.9532-0.40360.2312-1.609-1.32050.5302-0.79210.9467-0.27120.0660.6170.26981.717378.9565341.134912.8201
421.4219-1.5607-1.20223.56683.54853.6674-0.19440.66180.4372-0.4570.87830.3409-0.15020.08-0.48370.8414-0.5699-0.20050.8250.08961.78569.2665339.988411.8296
434.34461.8354-5.2483.0916-2.78268.5102-0.87690.1254-1.0309-0.38420.0742-0.11781.3115-0.40650.76711.1-0.4764-0.5220.35690.60122.072375.913327.400216.1289
449.0364-2.0846-2.33877.11670.46959.3303-0.42611.1338-1.72460.3237-0.87171.5885-0.0198-0.32561.05190.903-0.179-0.29110.84270.12991.939768.6068331.336413.7609
457.14545.8528-4.5338.1433-2.76995.1217-0.16770.66080.8418-0.61720.56930.25650.2254-0.8003-0.35570.8514-0.6743-0.15540.80890.43691.86469.5928334.40065.0135
466.46714.57485.65614.01594.06768.63511.35180.39190.30850.7338-0.65371.1782-0.395-0.6707-0.75560.7410.0690.42781.0529-0.06391.953561.8369346.415626.9286
473.6217-4.7449-3.27586.45285.31267.19740.8428-0.6132-0.06740.2137-0.37280.25320.9258-1.5494-0.32620.6243-0.29750.15231.1870.20711.744872.3975344.339725.2117
483.6587-1.34192.5388.96454.0414.72560.21591.38322.0829-0.8694-0.9825-0.1798-1.89150.810.78781.14260.0053-0.23080.71630.27381.191292.9176334.912319.0932
490.3176-0.5827-1.76621.06813.24269.83520.5446-0.16294.01750.7646-1.2408-3.571-4.26562.66670.64411.0343-0.45490.20720.7602-0.06012.301292.1226326.430331.031
504.0677-3.9604-5.5266.75756.97748.379-2.1417-1.11310.60873.81650.08891.23074.3551-0.65541.87871.4667-0.05850.32371.27910.02810.876382.5911335.330535.554
518.48176.2081-2.60138.4531-2.37984.3737-0.31280.42920.03430.1911-0.1997-1.5974-0.62420.60040.37850.6111-0.2492-0.22050.9080.30420.827883.0684327.301324.5431
524.74673.68991.80045.66552.08934.78630.5958-0.87460.62191.4552-1.25490.78750.2841-0.2820.41491.028-0.4945-0.06420.690.53582.292981.8739323.798928.0497
535.7543-0.8829-4.13691.7918-1.39255.4409-0.2833-1.1461.31581.49491.1315-2.05690.98430.8536-0.79851.0194-0.0143-0.48470.6877-0.06630.807484.5711332.338324.7169
546.5061-4.2543-1.5295.19792.07710.90580.27611.40231.6168-0.12580.00020.2836-0.4488-1.8509-0.11411.68530.63421.39433.145-0.12322.635534.1906441.598639.1952
556.90877.10246.60727.30396.78586.4215-1.3243-2.76597.67972.4927-0.59471.7424-8.1755-3.88921.98193.61990.35160.40012.4101-0.30893.164439.3073452.075740.1167
564.2213-3.4606-3.30894.70270.81074.5427-0.52220.30971.9523-0.9004-1.86642.8302-0.7609-1.47452.33882.84291.9994-0.25483.0587-0.36833.799642.3169446.774130.4377
570.1397-0.4352-0.16122.0514-0.461.45870.7366-0.4190.3162-0.13470.41810.9084-0.9464-0.2381-0.82171.39970.67630.55593.448-1.26723.971636.2507441.633235.376
580.49240.7414-0.46381.1094-0.69580.4381.93082.19664.4666-2.2098-2.2485-4.89030.66652.43330.46671.46460.85930.58513.8066-0.79693.582328.4983431.572126.7995
591.49680.8412-2.28633.82830.38154.3393-0.20321.13521.09140.83260.36110.0911-0.1409-1.632-0.12422.3961-0.2561.05621.47030.17112.580853.5129427.486537.6289
608.94756.8154-2.26975.1863-1.6118.2977-1.155-1.924-1.32790.28060.1530.65740.20981.57330.83793.02570.30811.47391.38420.12852.310876.7991423.904636.8916
615.9405-5.3653-4.6968.02527.036.162-1.2460.4872-2.1075-0.8219-0.5513-0.44461.2099-0.71711.60313.0882-0.09581.70821.5612-0.30613.430939.7169422.553572.4971
625.506-2.12295.25623.0620.77738.52081.1774-2.02870.89731.11460.50771.2454-0.944-2.5751-1.52062.5914-0.15841.94032.0595-0.07683.94935.601428.508568.2484
636.7443.10681.2332.677-1.83425.18820.2197-0.1064-0.3244-0.3391-0.71990.3312-1.1131-0.10070.50893.62380.20460.59341.32290.50722.771259.2628426.092661.5533
645.01094.54170.05724.3758-0.84193.0888-1.0195-0.2416-0.2423-0.0688-0.15011.2731.28390.16471.00972.7816-0.26321.10860.8342-0.16832.26166.1387419.194657.2969
653.3666-1.00120.0230.5008-0.4751.0809-0.4774-0.4425-0.20171.06010.18520.8615-0.4133-1.46160.46163.51660.18111.50863.0354-1.59583.670832.6124431.243476.3995
662.72612.64912.92134.06411.20414.92030.7201-1.5021.32770.6493-0.39681.63810.1773-1.7172-0.38062.0049-0.82621.06792.63420.11974.050831.154423.721584.9843
672.056-0.86650.75650.4057-0.28950.29761.0648-3.6309-0.2823.0170.14792.9444-1.3809-0.4322-1.0634.4224-1.1561.6982.93470.07533.033242.5382416.51580.7551
688.66473.8312-7.92151.7817-3.76658.04220.5033-0.32661.3554-4.02930.4667-4.2049-0.50891.2841-1.03633.5372-0.66931.68952.2382-0.32582.919245.6553428.536478.2256
694.5293-4.12596.14535.1423-4.73078.85710.4040.0316-0.2323-0.71860.53940.6312-0.4103-1.0458-1.12161.30180.1753-0.00530.93970.46532.094882.5395414.0272-26.404
705.6285-3.3352-3.16276.90584.26653.58870.78060.10390.8859-0.74240.60690.25-3.6522-1.074-1.07551.16670.02240.18370.7170.36471.69986.1545418.1187-19.7269
715.9992-3.93685.83517.6265-3.68359.7858-1.4342-0.36951.521.36630.8371.6482-2.7531-1.87520.61241.1390.2075-0.03760.9724-0.06722.844379.161422.1016-21.4609
725.1337-6.3935.92718.624-6.57027.902-0.157-0.39130.01620.23020.62462.1257-0.1621-0.1649-0.36221.3012-0.05420.07491.2435-0.12552.012875.3567412.2114-21.7865
738.6612.593-3.4659.89244.37774.6005-0.39431.23751.0002-2.7017-0.40732.6272-0.5298-1.62570.90931.4689-0.0809-0.42241.77210.47851.230471.4004411.8424-26.9259
741.70650.0119-0.0514-0.004-0.00070.0028-0.99280.0772-0.5030.50610.23180.0298-0.61310.58290.70911.650.16780.46540.94960.48611.711190.8776394.5473-14.6923
756.09066.37285.39539.15917.55516.19230.81360.2267-0.00841.00550.0239-0.90960.01270.5778-0.88721.2891-0.31050.06250.83090.30141.2145112.5457354.143729.7021
764.0511-0.8983-3.38895.1262-2.15754.43510.6476-1.08981.4147-0.4565-0.4317-0.5842-1.88191.322-0.10741.7251-0.6682-0.00561.2122-0.27921.5548122.46374.659854.3055
776.22055.322-5.39424.616-4.79345.18241.6478-1.2732-4.55540.515-1.8279-2.5560.4961.68280.05631.8257-0.27630.47011.51360.26473.559784.3067474.861734.5195
782.68670.4037-0.41810.1593-0.17030.1799-0.0119-0.05720.88930.2192-0.21580.6255-0.2105-0.20690.13321.357-1.04060.25281.8716-0.4252.455180.2859469.164137.8213
795.9261-3.83646.66148.5287-1.70398.5928-0.854-0.38751.61750.307-0.12761.1942-0.1956-0.71411.07461.77250.19270.90061.00610.02273.328878.5759476.737541.8227
806.1849-3.20744.16093.3191-4.21545.3650.2109-0.20991.42921.75080.28670.5771-0.9822-0.0633-0.3851.57210.25130.40381.55920.00752.03896.2729466.318652.1244
811.619-2.0312-1.70455.4855.25625.0980.7628-0.3506-0.02680.3223-0.54750.7983-0.922-0.1562-0.28661.78040.13220.32061.0417-0.1772.7165101.9594450.736557.0488
820.96930.50912.00635.8228-1.66315.4533-0.31730.1586-1.34191.4273-0.46810.27250.00390.35860.82271.46110.1940.22740.9295-0.15382.706497.336441.579745.7391
838.73972.09421.86075.17216.12767.3101-0.9216-1.2370.11680.57890.7627-0.4431.55650.7970.2014.1640.25440.86711.8658-1.00022.35684.9422421.225277.9001
842.41282.01442.06854.50495.36116.4521-1.1261.0676-3.6342-0.42670.9419-1.78371.1738-0.90860.26894.7138-0.91860.68611.9025-0.48082.670783.4997433.709881.4597
855.12191.72630.75630.6660.22220.1254-1.1351-0.94611.6706-0.1231-0.28351.1442-0.8254-0.28661.30614.0496-0.22670.47071.0434-0.23482.051980.7743429.440373.72
868.08224.9882-5.96596.1087-5.23465.1983-1.05891.2368-0.0485-1.990.422-0.4212-0.5882-1.60730.53544.277-0.28490.4272.1796-0.52321.508977.2922416.518270.3296
877.52560.02265.77833.4238-0.99185.2212-0.4875-0.43040.49621.907-0.46321.09381.09620.03340.74673.6209-0.45311.24021.171-0.04721.851767.4436417.682864.216
885.26253.4425-3.80553.3065-4.65927.68840.42731.3265-0.0019-3.9011.01012.03840.7095-1.4425-1.42252.3026-0.3656-0.34590.83880.42251.296890.7945342.4252-31.2268
896.76445.4448-3.46948.4371-4.82347.55390.59270.99580.22130.83420.71030.7987-0.43150.2637-1.18391.16770.1707-0.01740.81640.07660.831296.9322345.9376-23.5428
905.62863.6722-1.41163.2964-2.31175.11960.5485-0.09620.82121.13010.01781.0269-0.02590.6398-0.64050.8389-0.25340.04290.9567-0.07821.739899.3214344.693-13.0132
912.1242.659-2.5823.8204-3.94244.14530.4277-1.2426-1.7222-0.1534-0.3467-4.73312.09132.9939-0.04471.18250.3925-0.31931.6397-0.17272.0705103.4449331.964-20.2571
924.5633-4.727-0.68416.30922.52945.1887-0.6215-1.2059-0.09010.43610.0918-0.54220.2269-0.25830.19310.9719-0.43-0.31121.71590.9582.4547125.0423318.491358.7284
932.45360.96070.82281.71840.45270.2853-0.5661-0.4845-1.16050.14260.12020.92840.2676-0.72310.34250.7812-0.43750.04261.70181.03182.2854124.5442316.093854.1407
946.1771-4.9739-7.26794.7666.75559.642-0.2481-0.1282-0.88321.80830.43-0.67181.0426-0.6355-0.08391.3219-0.0325-0.25511.56740.90272.7458115.3378310.655364.059
954.3561-5.4677-1.98216.88952.87827.595-0.04990.48811.2790.3075-0.2402-1.0119-0.80770.32520.26421.3547-0.2379-0.46021.28630.62462.5147122.6081301.915649.0041
967.492-2.6475-5.50012.90462.8634.772-0.5367-2.0641-1.0620.9568-0.4949-0.89671.4158-0.49110.87751.0255-0.2137-0.11481.58290.61542.7099127.0652302.080560.0462
977.199-3.75774.44483.6666-0.89313.9480.70151.01750.7582-0.44640.144-1.1202-0.3325-0.2665-0.47470.55450.36670.00771.16820.38352.1129120.8814321.46214.8469
980.6141.84240.9287.23853.33568.07510.71220.4467-0.1866-0.2778-0.7111-0.43530.4970.1607-0.00040.77750.0598-0.23140.84080.1481.7897116.9669323.42397.6563
997.5972.67825.66754.05035.36167.8894-0.4494-0.5178-0.6719-0.78150.0678-0.7453-0.232-0.48850.411.08080.03860.22321.27580.03831.1859115.7067339.6507-1.0143
1006.39724.05738.53683.49045.85711.9987-0.1718-1.2372.14780.20310.09083.8353-1.2665-2.51960.25761.21180.26070.5081.61580.87663.293361.4414381.0371-20.3277
1014.16234.1933.43977.84515.25558.2919-0.6895-0.05360.4632-0.391-1.06434.023-0.2104-1.91931.66521.0676-0.3352-0.4263.04411.29533.080759.7116375.7225-28.2168
1025.66944.896-4.81344.8331-2.29129.8731-0.5126-0.5288-0.4533-0.008-0.2853-0.58593.03340.20310.67391.7144-0.1816-0.53661.04860.63332.596572.0513373.3942-33.7279
1034.7668-3.5989-0.19043.91012.16473.43220.25810.2122-0.0586-1.2271-0.33261.7296-1.6645-0.8595-0.09231.31140.22890.00540.90250.76223.01468.1631382.2733-31.4091
1042.68761.91741.91092.27760.5722.77350.6584-0.40344.02692.73560.22934.6731-3.2075-2.1005-0.9741.38250.09070.41150.94740.12311.844272.8232387.5318-23.0138
1059.87459.1183-7.5518.4529-6.97045.78050.47050.46080.67420.08290.68750.80780.4335-0.6054-1.04030.97310.015-0.25381.28290.37640.889974.2664376.8781-24.0315
1069.83-2.80392.34096.0725-1.97611.99230.6776-0.34951.9406-0.5072-1.4213-1.2565-0.51820.3470.7011.1533-0.1287-0.17241.00940.36091.925275.4807394.1213-27.6779
1076.33931.04342.53584.29793.80124.53970.79230.81-1.9204-0.7637-0.1214-0.06151.57970.1376-0.78284.0431-0.96430.62681.7142-0.86672.638488.446453.108971.9503
1086.0152-4.1079-3.1014.4576-0.61399.304-0.5228-3.20191.34222.7761-0.6170.81711.47071.51151.11944.5202-1.040.20232.7269-0.77621.3634101.7619452.576885.8488
1095.5567-2.04963.7067.20931.59143.82252.0944-0.3378-2.52322.6290.7201-4.32161.6981-1.353-2.75863.4295-0.4678-0.07961.3957-0.16692.3605108.2036448.165180.5519
1108.75131.9542-6.50492.2372-3.94448.28740.0459-2.1119-1.521710.6193-2.34691.6641.84530.21312.27383.37690.08920.4652.02660.36271.707696.3766447.919472.6666
1113.1699-3.20340.08923.276-0.06790.0152-0.0442-0.45980.55540.524-0.6214-1.00581.02-1.06370.51043.8089-0.3026-0.59131.4007-0.29672.1165105.0315451.355172.4138
1124.44042.17281.48491.07720.75310.5215-0.74460.44510.46170.43990.30760.2630.29020.40080.19592.982-0.2802-0.32931.7359-0.24622.1211104.3238442.78561.5445
1131.6640.8061.1012.13361.70983.95430.94090.0374-0.5949-0.0888-0.2324-0.7280.53140.1792-0.62290.68440.0285-0.54011.47110.49542.3906159.8052309.179223.4052
1141.0828-1.258-0.99311.46091.15520.9117-0.4288-2.9572-3.88633.58141.79351.69670.5273-1.332-1.4062.0532-0.1289-0.72081.45830.90042.0734149.8132306.734428.3937
1155.8227-6.8784-6.21938.17517.10557.51560.16540.75860.0042-1.2653-1.48460.8504-2.6742-2.01461.29131.30040.4365-0.65430.96440.1852.7191149.3884304.405311.7715
1166.43044.7053-5.55297.8119-1.33826.4973-2.65160.3335-4.2996-0.463-0.451-0.84582.77211.69532.78571.13440.23870.11641.3817-0.14762.6185153.866294.10593.8103
1175.1043-3.3571-0.47328.75141.66061.33060.0734-0.34250.80820.39680.7318-2.5666-0.30780.7571-0.92521.4130.91120.5281.5455-0.59162.582275.8571451.268945.8194
1185.9896-4.64550.51433.9169-1.13848.5725-1.0212-1.6253-2.14460.89911.54255.11940.0812-3.3441-0.47110.9855-0.02840.55232.1149-0.21012.840271.1701447.889347.9336
1194.7145-3.26962.5425.18051.37774.7536-1.86820.681-4.4175-1.7006-0.0397-2.88033.81212.28341.74942.07050.87010.89072.27840.09362.632867.6044453.913654.0668
1206.01051.15534.28061.64691.67116.5365-0.0865-0.0054-0.45520.1919-0.0276-0.50150.36230.9298-0.08290.2981-0.189-0.09830.6316-0.05680.6751129.6055338.439541.4982
1211.11730.2742-0.58132.873-2.20781.7978-0.07070.40980.40671.03330.0288-0.7354-1.25560.44820.00382.0822-0.38330.00921.2637-0.24142.055117.3063399.135149.3157
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)
120X-RAY DIFFRACTION120chain 'a' and (resseq 1:6)
121X-RAY DIFFRACTION121chain 'W' and (resseq 1:72)

+
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