5W79 | pdb_00005w79

Crystal Structure of the Group II Chaperonin from Methanococcus Maripaludis, Cysteine-less mutant in the Apo State

• PDB DOI: https://doi.org/10.2210/pdb5W79/pdb

• Classification: CHAPERONE
• Organism(s): Methanococcus maripaludis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2017-06-19 Released: 2018-06-20 
• Deposition Author(s): Dalton, K.M., Lopez, T., Liu, C., Ralston, C.Y., Pereira, J.H., Chartron, J.W., McAndrew, R.P., Douglas, N.R., Adams, P.D., Pande, V.S., Frydman, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free: 
  0.281 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Literature

The Conformational Cycle of the Group II Chaperonin Termini

Dalton, K.M., Lopez, T., Liu, C., Ralston, C.Y., Pereira, J.H., Chartron, J.W., McAndrew, R.P., Douglas, N.R., Adams, P.D., Pande, V.S., Frydman, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C8  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 468.05 kDa 
• Atom Count: 31,143 
• Modeled Residue Count: 4,120 
• Deposited Residue Count: 4,344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin	A, B, C, D, E, F, G, H	543	Methanococcus maripaludis	Mutation(s): 8  EC: 3.6.1 (UniProt), 5.6.1.7 (UniProt)
UniProt
Find proteins for Q6LX38 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL)) Explore Q6LX38  Go to UniProtKB:  Q6LX38

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free:  0.281 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.98	α = 90
b = 149.98	β = 90
c = 416.477	γ = 120

Software Package:

Software Name	Purpose
iMOSFLM	data processing
SCALA	data reduction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Dalton, K.M., Lopez, T., Liu, C., Ralston, C.Y., Pereira, J.H., Chartron, J.W., McAndrew, R.P., Douglas, N.R., Adams, P.D., Pande, V.S., Frydman, J.

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2018-08-29
  Changes: Data collection, Database references
• Version 1.2: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary