3BIO | pdb_00003bio

Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83

• PDB DOI: https://doi.org/10.2210/pdb3BIO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Porphyromonas gingivalis W83
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-11-30 Released: 2007-12-25 
• Deposition Author(s): Nocek, B., Mulligan, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.187 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83.

Nocek, B., Mulligan, R., Moy, S., Joachimiak, A.

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)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.28 kDa 
• Atom Count: 4,891 
• Modeled Residue Count: 581 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, Gfo/Idh/MocA family	A, B	304	Porphyromonas gingivalis W83	Mutation(s): 0  Gene Names: PG_0806 EC: 1.4.1.16
UniProt
Find proteins for Q7MW40 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MW40  Go to UniProtKB:  Q7MW40

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A], F [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.80 Å
• R-Value Free:  0.187 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.268	α = 90
b = 99.268	β = 90
c = 356.025	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
Coot	model building
MLPHARE	phasing
PHENIX	phasing
REFMAC	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-25 
Deposition Author(s): Nocek, B., Mulligan, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-12-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary