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)

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)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 79.49 kDa
Atom Count: 5,506
Modeled Residue Count: 678
Deposited Residue Count: 698
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MXM8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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Entry History

Deposition Data

Released Date: 2005-04-19

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.