3E10 | pdb_00003e10

Crystal structure of Putative NADH Oxidase (NP_348178.1) from CLOSTRIDIUM ACETOBUTYLICUM at 1.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3E10/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium acetobutylicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-01 Released: 2008-08-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Literature

Crystal structure of Putative NADH Oxidase (NP_348178.1) from CLOSTRIDIUM ACETOBUTYLICUM at 1.40 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)

Macromolecule Content 

• Total Structure Weight: 41.3 kDa 
• Atom Count: 3,513 
• Modeled Residue Count: 333 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative NADH Oxidase	A, B	168	Clostridium acetobutylicum	Mutation(s): 0  Gene Names: NP_348178.1, CA_C1551
UniProt
Find proteins for Q97IT9 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97IT9  Go to UniProtKB:  Q97IT9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], L [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
EPE	D [auth A], K [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 1.40 Å
• R-Value Free:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33E10

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.077	α = 90
b = 83.528	β = 90
c = 51.891	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary