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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of chaperonin GroEL from

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D7  (Explore in 3D)
Global Stoichiometry: Homo 14-mer - A14 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D7  (Explore in 3D)
Global Stoichiometry: Homo 14-mer - A14 

Biological assembly 2 assigned by authors and generated by PISA (software)

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60 kDa chaperonin	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	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
CA	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
MG	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (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

Entry History 

Deposition Data

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

Revision History  

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