3MCW | pdb_00003mcw

Crystal structure of an a putative hydrolase of the isochorismatase family (CV_1320) from Chromobacterium violaceum ATCC 12472 at 1.06 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 
    0.151 (Depositor), 0.150 (DCC) 
  • R-Value Work: 
    0.131 (Depositor), 0.131 (DCC) 
  • R-Value Observed: 
    0.132 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3MCW

This is version 1.6 of the entry. See complete history. 

Literature

Crystal structure of an a putative hydrolase of the isochorismatase family (CV_1320) from Chromobacterium violaceum ATCC 12472 at 1.06 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 44.4 kDa 
  • Atom Count: 3,700 
  • Modeled Residue Count: 388 
  • Deposited Residue Count: 396 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative hydrolase
A, B
198Chromobacterium violaceum ATCC 12472Mutation(s): 0 
Gene Names: CV_1320
UniProt
Find proteins for Q7NYF4 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK))
Explore Q7NYF4 
Go to UniProtKB:  Q7NYF4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NYF4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD


Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO

Query on EDO


Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
Q [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free:  0.151 (Depositor), 0.150 (DCC) 
  • R-Value Work:  0.131 (Depositor), 0.131 (DCC) 
  • R-Value Observed: 0.132 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.697α = 90
b = 60.85β = 102.97
c = 71.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata 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: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-10-30
    Changes: Data collection, Structure summary
  • Version 1.6: 2025-10-22
    Changes: Structure summary