3PZL | pdb_00003pzl

The crystal structure of agmatine ureohydrolase of Thermoplasma volcanium

• PDB DOI: https://doi.org/10.2210/pdb3PZL/pdb

• Classification: HYDROLASE
• Organism(s): Thermoplasma volcanium GSS1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-14 Released: 2011-01-19 
• Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

The crystal structure of agmatine ureohydrolase of Thermoplasma volcanium

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.43 kDa 
• Atom Count: 6,896 
• Modeled Residue Count: 873 
• Deposited Residue Count: 939 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agmatine ureohydrolase	A, B, C	313	Thermoplasma volcanium GSS1	Mutation(s): 0  Gene Names: TV0538, TVG0528110
UniProt
Find proteins for Q97BB8 (Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)) Explore Q97BB8  Go to UniProtKB:  Q97BB8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.139	α = 90
b = 95.139	β = 90
c = 198.375	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary