1ZBR | pdb_00001zbr

Crystal Structure of the Putative Arginine Deiminase from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR3

• PDB DOI: https://doi.org/10.2210/pdb1ZBR/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Porphyromonas gingivalis W83
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-04-08 Released: 2005-04-19 
• Deposition Author(s): Forouhar, F., Chen, Y., Kuzin, A., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.289 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Crystal Structure of the Putative Arginine Deiminase from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR3

Forouhar, F., Chen, Y., Kuzin, A., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

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: 79.49 kDa 
• Atom Count: 5,506 
• Modelled Residue Count: 678 
• Deposited Residue Count: 698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein	A, B	349	Porphyromonas gingivalis W83	Mutation(s): 7  Gene Names: locus_tag="PG0144"
UniProt
Find proteins for Q7MXM8 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MXM8  Go to UniProtKB:  Q7MXM8

Small Molecules

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: 2.60 Å
• R-Value Free:  0.289 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.824	α = 90
b = 86.049	β = 90
c = 144.641	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-19 
Deposition Author(s): Forouhar, F., Chen, Y., Kuzin, A., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary