[English] 日本語
Yorodumi
- PDB-10yy: Crystal Structure of the Chaperonin GroEL apical domain from Bord... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 10yy
TitleCrystal Structure of the Chaperonin GroEL apical domain from Bordetella pertussis
ComponentsChaperonin GroEL
KeywordsCHAPERONE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Chaperonin / GroEL
Function / homology
Function and homology information


chaperonin ATPase / isomerase activity / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / ATP binding / cytoplasm
Similarity search - Function
Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of the Chaperonin GroEL apical domain from Bordetella pertussis
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionFeb 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperonin GroEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0932
Polymers21,0581
Non-polymers351
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.768, 145.768, 34.858
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

-
Components

#1: Protein Chaperonin GroEL / 60 kDa chaperonin / Chaperonin-60 / Cpn60


Mass: 21058.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Gene: groEL, cpn60, groL, mopA, BP3495 / Plasmid: BopeA.17935.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P48210, chaperonin ATPase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 75.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: JCSG+ D12: 0.04M Potassium phosphate monobasic, 16% PEG 6000. plate 20567 D12 drop 1, Puck: PSL-1601, Cryo: 80% crystallant + 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jan 31, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.95→47.71 Å / Num. obs: 9287 / % possible obs: 99.9 % / Redundancy: 20.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.041 / Rrim(I) all: 0.182 / Χ2: 1.25 / Net I/σ(I): 15.3 / Num. measured all: 187564
Reflection shellResolution: 2.95→3.13 Å / % possible obs: 99.9 % / Redundancy: 21.5 % / Rmerge(I) obs: 2.224 / Num. measured all: 31738 / Num. unique obs: 1477 / CC1/2: 0.886 / Rpim(I) all: 0.49 / Rrim(I) all: 2.278 / Χ2: 1.07 / Net I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
PHENIX(2.0_5936: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→47.71 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 471 5.1 %
Rwork0.2129 --
obs0.2148 9243 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 1 0 1380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061392
X-RAY DIFFRACTIONf_angle_d0.7881885
X-RAY DIFFRACTIONf_dihedral_angle_d21.671523
X-RAY DIFFRACTIONf_chiral_restr0.048227
X-RAY DIFFRACTIONf_plane_restr0.006248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.380.37581740.32892844X-RAY DIFFRACTION99
3.38-4.250.26021460.24072922X-RAY DIFFRACTION100
4.26-47.710.21591510.17813006X-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)
12.4857-0.9098-0.20362.39420.33880.71220.4307-0.17410.64340.7442-0.21070.7721-0.6141-0.81250.01991.51260.19170.06330.7441-0.02841.07964.7426-11.679313.0432
23.5655-1.06650.6710.7609-0.50437.2836-0.2312-0.46310.5945-0.28950.205-0.5136-0.91130.235-0.02871.2533-0.0320.03220.50850.03450.90175.401-17.68569.2185
33.8926-0.98250.64693.4192-1.09464.28750.29090.9956-0.2209-0.4025-0.3996-0.7283-0.18171.86750.00191.3621-0.39870.15060.93830.16641.108383.4405-15.13222.474
42.50012.53990.19643.87941.08973.43080.1507-0.20980.17880.4294-0.1033-0.2763-0.8894-0.087-0.02251.1872-0.03910.00620.4575-0.01590.709974.657-16.302712.0948
53.67254.48293.19426.30585.3715.5940.3584-1.0957-0.83730.28730.0554-1.63970.2844-1.1338-0.51021.13480.0253-0.11630.88980.11651.091680.3331-28.112513.2996
62.12161.4795-0.81456.43110.00773.86380.1505-0.1273-0.0825-0.5475-0.20270.1821-0.088-0.05510.13141.01230.02940.01440.65120.02250.749871.6341-22.57117.6141
72.99171.15071.48112.30120.71196.3649-0.1141-0.24550.26090.25020.268-0.2397-0.3155-0.2716-0.01711.05560.0201-0.00940.7274-0.01770.680663.6246-34.258123.7919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 191 through 212 )
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 229 )
3X-RAY DIFFRACTION3chain 'A' and (resid 230 through 243 )
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 295 )
5X-RAY DIFFRACTION5chain 'A' and (resid 296 through 305 )
6X-RAY DIFFRACTION6chain 'A' and (resid 306 through 338 )
7X-RAY DIFFRACTION7chain 'A' and (resid 339 through 374 )

+
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