3OVG

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

• PDB DOI:  https://doi.org/10.2210/pdb3OVG/pdb

• Classification: HYDROLASE
• Organism(s): Mycoplasmopsis synoviae 53
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-09-16 Released: 2010-10-13 
• Deposition Author(s): Zhang, Z., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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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 

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 248.2 kDa 
• Atom Count: 17,874 
• Modelled Residue Count: 2,106 
• Deposited Residue Count: 2,178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
amidohydrolase	A, B, C, D, E, F	363	Mycoplasmopsis synoviae 53	Mutation(s): 0  Gene Names: had, MS53_0025 EC: 3.1.1.104 (UniProt), 3.1.1.25 (UniProt)
UniProt
Find proteins for Q4A724 (Mycoplasmopsis synoviae (strain 53)) Explore Q4A724  Go to UniProtKB:  Q4A724

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	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
ZN	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

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D, E, F	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 89.256	α = 98.95
b = 89.186	β = 92.89
c = 96.059	γ = 119.86

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-13 
Deposition Author(s): Zhang, Z., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• 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
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description