5DA8 | pdb_00005da8

Crystal structure of chaperonin GroEL from

PDB DOI: https://doi.org/10.2210/pdb5DA8/pdb

Classification: CHAPERONE
Organism(s): Chlorobaculum tepidum TLS
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-08-19 Released: 2015-10-14
Deposition Author(s): Chang, C., Marshall, N., Feldmann, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.230 (Depositor), 0.231 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of chaperonin GroEL from

Chang, C., Marshall, N., Feldmann, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 1,631.26 kDa
Atom Count: 99,552
Modeled Residue Count: 13,984
Deposited Residue Count: 15,260
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60 kDa chaperonin	A AA [auth a] B BA [auth b] C A, AA [auth a], B, BA [auth b], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	545	Chlorobaculum tepidum TLS	Mutation(s): 0 Gene Names: groL, groEL, CT0530 EC: 5.6.1.7
UniProt
Find proteins for Q8KF02 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)) Explore Q8KF02 Go to UniProtKB: Q8KF02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KF02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain ZA [auth P] SDF format, chain XA [auth N] SDF format, chain VB [auth b] SDF format, chain VA [auth M] SDF format, chain TB [auth a] SDF format, chain TA [auth L] SDF format, chain RB [auth Z] SDF format, chain RA [auth K] SDF format, chain PB [auth Y] SDF format, chain PA [auth J] SDF format, chain NB [auth V] SDF format, chain LA [auth G] SDF format, chain KB [auth U] SDF format, chain JA [auth F] SDF format, chain IB [auth T] SDF format, chain IA [auth E] SDF format, chain HA [auth D] SDF format, chain GA [auth C] SDF format, chain EB [auth R] SDF format, chain EA [auth B] SDF format, chain CA [auth A] MOL2 format, chain ZA [auth P] MOL2 format, chain XA [auth N] MOL2 format, chain VB [auth b] MOL2 format, chain VA [auth M] MOL2 format, chain TB [auth a] MOL2 format, chain TA [auth L] MOL2 format, chain RB [auth Z] MOL2 format, chain RA [auth K] MOL2 format, chain PB [auth Y] MOL2 format, chain PA [auth J] MOL2 format, chain NB [auth V] MOL2 format, chain LA [auth G] MOL2 format, chain KB [auth U] MOL2 format, chain JA [auth F] MOL2 format, chain IB [auth T] MOL2 format, chain IA [auth E] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain EB [auth R] MOL2 format, chain EA [auth B] MOL2 format, chain CA [auth A] mmCIF format, chain ZA [auth P] mmCIF format, chain XA [auth N] mmCIF format, chain VB [auth b] mmCIF format, chain VA [auth M] mmCIF format, chain TB [auth a] mmCIF format, chain TA [auth L] mmCIF format, chain RB [auth Z] mmCIF format, chain RA [auth K] mmCIF format, chain PB [auth Y] mmCIF format, chain PA [auth J] mmCIF format, chain NB [auth V] mmCIF format, chain LA [auth G] mmCIF format, chain KB [auth U] mmCIF format, chain JA [auth F] mmCIF format, chain IB [auth T] mmCIF format, chain IA [auth E] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain EB [auth R] mmCIF format, chain EA [auth B] mmCIF format, chain CA [auth A]	CA [auth A] EA [auth B] EB [auth R] GA [auth C] HA [auth D] CA [auth A], EA [auth B], EB [auth R], GA [auth C], HA [auth D], IA [auth E], IB [auth T], JA [auth F], KB [auth U], LA [auth G], NB [auth V], PA [auth J], PB [auth Y], RA [auth K], RB [auth Z], TA [auth L], TB [auth a], VA [auth M], VB [auth b], XA [auth N], ZA [auth P]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth A] Focus chain EA [auth B] Focus chain EB [auth R] Focus chain GA [auth C] Focus chain HA [auth D] Focus chain IA [auth E] Focus chain IB [auth T] Focus chain JA [auth F] Focus chain KB [auth U] Focus chain LA [auth G] Focus chain NB [auth V] Focus chain PA [auth J] Focus chain PB [auth Y] Focus chain RA [auth K] Focus chain RB [auth Z] Focus chain TA [auth L] Focus chain TB [auth a] Focus chain VA [auth M] Focus chain VB [auth b] Focus chain XA [auth N] Focus chain ZA [auth P] Interactions & Density Focus chain CA [auth A] Focus chain EA [auth B] Focus chain EB [auth R] Focus chain GA [auth C] Focus chain HA [auth D] Focus chain IA [auth E] Focus chain IB [auth T] Focus chain JA [auth F] Focus chain KB [auth U] Focus chain LA [auth G] Focus chain NB [auth V] Focus chain PA [auth J] Focus chain PB [auth Y] Focus chain RA [auth K] Focus chain RB [auth Z] Focus chain TA [auth L] Focus chain TB [auth a] Focus chain VA [auth M] Focus chain VB [auth b] Focus chain XA [auth N] Focus chain ZA [auth P]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain YA [auth O] SDF format, chain WA [auth M] SDF format, chain UB [auth a] SDF format, chain SB [auth Z] SDF format, chain SA [auth K] SDF format, chain QB [auth Y] SDF format, chain QA [auth J] SDF format, chain OB [auth V] SDF format, chain OA [auth I] SDF format, chain MA [auth G] SDF format, chain LB [auth U] SDF format, chain KA [auth F] SDF format, chain JB [auth T] SDF format, chain FB [auth R] SDF format, chain FA [auth B] SDF format, chain DA [auth A] SDF format, chain CB [auth Q] SDF format, chain AB [auth P] MOL2 format, chain YA [auth O] MOL2 format, chain WA [auth M] MOL2 format, chain UB [auth a] MOL2 format, chain SB [auth Z] MOL2 format, chain SA [auth K] MOL2 format, chain QB [auth Y] MOL2 format, chain QA [auth J] MOL2 format, chain OB [auth V] MOL2 format, chain OA [auth I] MOL2 format, chain MA [auth G] MOL2 format, chain LB [auth U] MOL2 format, chain KA [auth F] MOL2 format, chain JB [auth T] MOL2 format, chain FB [auth R] MOL2 format, chain FA [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain CB [auth Q] MOL2 format, chain AB [auth P] mmCIF format, chain YA [auth O] mmCIF format, chain WA [auth M] mmCIF format, chain UB [auth a] mmCIF format, chain SB [auth Z] mmCIF format, chain SA [auth K] mmCIF format, chain QB [auth Y] mmCIF format, chain QA [auth J] mmCIF format, chain OB [auth V] mmCIF format, chain OA [auth I] mmCIF format, chain MA [auth G] mmCIF format, chain LB [auth U] mmCIF format, chain KA [auth F] mmCIF format, chain JB [auth T] mmCIF format, chain FB [auth R] mmCIF format, chain FA [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain CB [auth Q] mmCIF format, chain AB [auth P]	AB [auth P] CB [auth Q] DA [auth A] FA [auth B] FB [auth R] AB [auth P], CB [auth Q], DA [auth A], FA [auth B], FB [auth R], JB [auth T], KA [auth F], LB [auth U], MA [auth G], OA [auth I], OB [auth V], QA [auth J], QB [auth Y], SA [auth K], SB [auth Z], UB [auth a], WA [auth M], YA [auth O]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth P] Focus chain CB [auth Q] Focus chain DA [auth A] Focus chain FA [auth B] Focus chain FB [auth R] Focus chain JB [auth T] Focus chain KA [auth F] Focus chain LB [auth U] Focus chain MA [auth G] Focus chain OA [auth I] Focus chain OB [auth V] Focus chain QA [auth J] Focus chain QB [auth Y] Focus chain SA [auth K] Focus chain SB [auth Z] Focus chain UB [auth a] Focus chain WA [auth M] Focus chain YA [auth O] Interactions & Density Focus chain AB [auth P] Focus chain CB [auth Q] Focus chain DA [auth A] Focus chain FA [auth B] Focus chain FB [auth R] Focus chain JB [auth T] Focus chain KA [auth F] Focus chain LB [auth U] Focus chain MA [auth G] Focus chain OA [auth I] Focus chain OB [auth V] Focus chain QA [auth J] Focus chain QB [auth Y] Focus chain SA [auth K] Focus chain SB [auth Z] Focus chain UB [auth a] Focus chain WA [auth M] Focus chain YA [auth O]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain UA [auth M] SDF format, chain NA [auth H] SDF format, chain MB [auth V] SDF format, chain HB [auth T] SDF format, chain GB [auth S] SDF format, chain DB [auth R] SDF format, chain BB [auth Q] MOL2 format, chain UA [auth M] MOL2 format, chain NA [auth H] MOL2 format, chain MB [auth V] MOL2 format, chain HB [auth T] MOL2 format, chain GB [auth S] MOL2 format, chain DB [auth R] MOL2 format, chain BB [auth Q] mmCIF format, chain UA [auth M] mmCIF format, chain NA [auth H] mmCIF format, chain MB [auth V] mmCIF format, chain HB [auth T] mmCIF format, chain GB [auth S] mmCIF format, chain DB [auth R] mmCIF format, chain BB [auth Q]	BB [auth Q] DB [auth R] GB [auth S] HB [auth T] MB [auth V] BB [auth Q], DB [auth R], GB [auth S], HB [auth T], MB [auth V], NA [auth H], UA [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth Q] Focus chain DB [auth R] Focus chain GB [auth S] Focus chain HB [auth T] Focus chain MB [auth V] Focus chain NA [auth H] Focus chain UA [auth M] Interactions & Density Focus chain BB [auth Q] Focus chain DB [auth R] Focus chain GB [auth S] Focus chain HB [auth T] Focus chain MB [auth V] Focus chain NA [auth H] Focus chain UA [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.263 (Depositor), 0.263 (DCC)
R-Value Work: 0.230 (Depositor), 0.231 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.996	α = 75.46
b = 159.781	β = 90.51
c = 228.823	γ = 91.22

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing
SBC-Collect	data collection

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description