2R6H | pdb_00002r6h

Crystal structure of the domain comprising the NAD binding and the FAD binding regions of the NADH:ubiquinone oxidoreductase, Na translocating, F subunit from Porphyromonas gingivalis

• PDB DOI: https://doi.org/10.2210/pdb2R6H/pdb

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


• Deposited: 2007-09-05 Released: 2007-09-11 
• Deposition Author(s): Kim, Y., Mulligan, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Crystal Structure of the Domain Comprising the Regions Binding NAD and FAD from the NADH:Ubiquinone Oxidoreductase, Na Translocating, F Subunit from Porphyromonas gingivalis.

Kim, Y., Mulligan, R., Moy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 139.48 kDa 
• Atom Count: 9,919 
• Modeled Residue Count: 1,144 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase, Na translocating, F subunit	A, B, C, D	290	Porphyromonas gingivalis W83	Mutation(s): 0  Gene Names: nqrF, PG_2177 EC: 1.6.5 (PDB Primary Data), 7.2.1.1 (UniProt)
UniProt
Find proteins for Q7MT22 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MT22  Go to UniProtKB:  Q7MT22

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	H [auth A], K [auth B], P [auth C], S [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], N [auth C], O [auth C], Q [auth D], R [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.681	α = 90
b = 175.681	β = 90
c = 244.292	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-2000	data collection
SHARP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Kim, Y., Mulligan, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary