3OVG

The crystal structure of an amidohydrolase from Mycoplasma synoviae with Zn ion bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of an amidohydrolase from Mycoplasma synoviae with Zn ion bound

Zhang, Z.Kumaran, D.Burley, S.K.Swaminathan, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
amidohydrolaseA, B, C, D, E, F363Mycoplasma synoviae 53Mutation(s): 0 
Gene Names: hadMS53_0025
EC: 3.1.1.25
Find proteins for Q4A724 (Mycoplasma synoviae (strain 53))
Explore Q4A724 
Go to UniProtKB:  Q4A724
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , J [auth B] , K [auth B] , M [auth C] , N [auth C] , P [auth D] , Q [auth D] , 
G [auth A],  H [auth A],  J [auth B],  K [auth B],  M [auth C],  N [auth C],  P [auth D],  Q [auth D],  S [auth E],  T [auth E],  V [auth F],  W [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E, FL-PEPTIDE LINKINGC7 H14 N2 O4LYS
MSE
Query on MSE
A, B, C, D, E, FL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.256α = 98.95
b = 89.186β = 92.89
c = 96.059γ = 119.86
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-22
    Changes: Structure summary
  • Version 1.3: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary