5W74

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperonin
A, B, C, D, E
A, B, C, D, E, F, G, H
543Methanococcus maripaludisMutation(s): 1 
UniProt
Find proteins for Q877G8 (Methanococcus maripaludis)
Explore Q877G8 
Go to UniProtKB:  Q877G8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ877G8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
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
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
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 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.72α = 90
b = 221.93β = 90
c = 262.15γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata processing
Aimlessdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE- SC0008504
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM074074
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM062868
National Institutes of Health/National Eye Institute (NIH/NEI)United States2PN2EY016525.
Department of Energy (DOE, United States)United StatesDE-AC02- 05CH11231.

Revision History  (Full details and data files)

  • 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