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

• PDB DOI: https://doi.org/10.2210/pdb3MCW/pdb

• Classification: HYDROLASE
• Organism(s): Chromobacterium violaceum ATCC 12472
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-29 Released: 2010-06-23 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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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) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hydrolase	A, B	198	Chromobacterium violaceum ATCC 12472	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	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	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
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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) 

Diffraction Data: https://doi.org/10.18430/M33MCW

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.697	α = 90
b = 60.85	β = 102.97
c = 71.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• 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