3LWX

Crystal structure of Na(+)-translocating NADH-quinone reductase subunit C (YP_001302508.1) from Parabacteroides distasonis ATCC 8503 at 1.10 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3LWX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Parabacteroides distasonis ATCC 8503
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-24 Released: 2010-03-31 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.138 
• R-Value Work: 0.116 
• R-Value Observed: 0.117 

Literature

Crystal structure of Na(+)-translocating NADH-quinone reductase subunit C (YP_001302508.1) from Parabacteroides distasonis ATCC 8503 at 1.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.1 kDa 
• Atom Count: 2,238 
• Modelled Residue Count: 199 
• Deposited Residue Count: 199 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase, Na translocating, C subunit	A	199	Parabacteroides distasonis ATCC 8503	Mutation(s): 0  Gene Names: BDI_1123 EC: 7.2.1.1
UniProt
Find proteins for A6LB22 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LB22  Go to UniProtKB:  A6LB22

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.10 Å
• R-Value Free: 0.138 
• R-Value Work: 0.116 
• R-Value Observed: 0.117 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M33LWX

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.444	α = 90
b = 60.693	β = 90
c = 82.758	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Data collection, Structure summary