5W74

Crystal Structure of the Group II Chaperonin from Methanococcus Maripaludis D386ADeltaLid Mutant in the Open, ADP-Bound State

• PDB DOI: https://doi.org/10.2210/pdb5W74/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.
• Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Eye Institute (NIH/NEI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free: 
  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.265 (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: Dihedral - D8  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

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

Macromolecule Content

• Total Structure Weight: 469.58 kDa 
• Atom Count: 28,632 
• Modelled Residue Count: 3,816 
• 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): 1
UniProt
Find proteins for Q877G8 (Methanococcus maripaludis) Explore Q877G8  Go to UniProtKB:  Q877G8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.265 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.72	α = 90
b = 221.93	β = 90
c = 262.15	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

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.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE- SC0008504
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM074074
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM062868
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	2PN2EY016525.
Department of Energy (DOE, United States)	United States	DE-AC02- 05CH11231.

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: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations