2D9R | pdb_00002d9r

Structure of Conserved Protein of Unknown Function PG0164 from Porphyromonas gingivalis [W83]

• PDB DOI: https://doi.org/10.2210/pdb2D9R/pdb

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


• Deposited: 2005-12-13 Released: 2006-01-24 
• Deposition Author(s): Binkowski, T.A., Hatzos, C., Moy, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.227 (Depositor) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Conserved hypothetical protein PG0164 frpm Porphyromonas gingivalis [W83]

Binkowski, T.A., Hatzos, C., Moy, S., Collart, F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.76 kDa 
• Atom Count: 762 
• Modelled Residue Count: 85 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein	A	104	Porphyromonas gingivalis W83	Mutation(s): 3  Gene Names: PG0164
UniProt
Find proteins for Q7MXL1 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MXL1  Go to UniProtKB:  Q7MXL1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.227 (Depositor) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.631	α = 90
b = 50.631	β = 90
c = 68.651	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-24 
Deposition Author(s): Binkowski, T.A., Hatzos, C., Moy, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-01-24
  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: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary