6KFV | pdb_00006kfv

GroEL from Xanthomonas oryzae pv. oryzae

• PDB DOI: https://doi.org/10.2210/pdb6KFV/pdb

• Classification: CHAPERONE
• Organism(s): Xanthomonas oryzae pv. oryzae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-07-08 Released: 2020-07-08 
• Deposition Author(s): Tran, H.T., Lee, J.H., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free: 
  0.304 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Chaperonin GroEL from Xanthomonas oryzae pv. oryzae

Tran, H.T., Lee, J., Park, H., Kim, J.G., Kim, S., Ahn, Y.J., Kang, L.W.

(2019) Crystals (Basel) 9

• DOI: https://doi.org/10.3390/cryst9080399

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)

Macromolecule Content 

• Total Structure Weight: 773.21 kDa 
• Atom Count: 53,933 
• Modeled Residue Count: 7,342 
• Deposited Residue Count: 7,350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60 kDa chaperonin	A, B, C, D, E, F, G, H, I, J, K, L, M, N	525	Xanthomonas oryzae pv. oryzae	Mutation(s): 0  Gene Names: groL, groEL, BCR61_23115, EYR02_02960, EYR03_02675 EC: 5.6.1.7
UniProt
Find proteins for Q5GUT1 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5GUT1  Go to UniProtKB:  Q5GUT1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	R [auth I], S [auth K]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)	O [auth B], P [auth F], Q [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free:  0.304 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.092	α = 90
b = 239.5	β = 90
c = 278.253	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Tran, H.T., Lee, J.H., Kang, L.W.

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2022-01-19
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Refinement description