3D4R

CRYSTAL STRUCTURE OF a DUF2118 family protein (MMP0046) FROM METHANOCOCCUS MARIPALUDIS AT 2.20 A RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of Domain of Unknown Function from the Pfam-B_34464 Family (NP_987166.1) from Methanococcus maripaludis JJ (DSM 2067) at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Domain of Unknown Function from the Pfam-B_34464 Family
A, B, C, D, E
A, B, C, D, E, F
169Methanococcus maripaludisMutation(s): 0 
Gene Names: NP_987166.1, MMP0046
UniProt
Find proteins for Q6M171 (Methanococcus maripaludis (strain S2 / LL))
Explore Q6M171 
Go to UniProtKB:  Q6M171
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6M171
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
L [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth C]
J [auth C]
K [auth D]
G [auth A],
H [auth A],
I [auth C],
J [auth C],
K [auth D],
M [auth E],
N [auth E],
O [auth F],
P [auth F],
Q [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.877α = 90
b = 109.858β = 90
c = 135.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations