3M5K | pdb_00003m5k

Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (BDI_1728) from Parabacteroides distasonis ATCC 8503 at 1.86 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3M5K/pdb

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


• Deposited: 2010-03-12 Released: 2010-05-05 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.178 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.160 (Depositor) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (BDI_1728) from Parabacteroides distasonis ATCC 8503 at 1.86 A resolution

Joint Center for Structural Genomics (JCSG)

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 Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 40.91 kDa 
• Atom Count: 3,443 
• Modeled Residue Count: 336 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative NADH dehydrogenase/NAD(P)H nitroreductase	A, B	172	Parabacteroides distasonis ATCC 8503	Mutation(s): 0  Gene Names: BDI_1728
UniProt
Find proteins for A6LCR1 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LCR1  Go to UniProtKB:  A6LCR1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], E [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
CL	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL	D [auth A], F [auth B]	Unknown ligand VEXZGXHMUGYJMC-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: 1.86 Å
• R-Value Free:  0.178 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.160 (Depositor) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33M5K

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.639	α = 90
b = 149.639	β = 90
c = 149.639	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: 2010-05-05 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, 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: 2024-10-09
  Changes: Data collection, Refinement description, Structure summary