1XHC | pdb_00001xhc

NADH oxidase /nitrite reductase from Pyrococcus furiosus Pfu-1140779-001

• PDB DOI: https://doi.org/10.2210/pdb1XHC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-17 Released: 2004-11-23 
• Deposition Author(s): Horanyi, P., Tempel, W., Weinberg, M.V., Liu, Z.-J., Shah, A., Chen, L., Lee, D., Sugar, F.J., Brereton, P.S., Izumi, M., Poole II, F.L., Shah, C., Jenney Jr., F.E., Arendall III, W.B., Rose, J.P., Adams, M.W.W., Richardson, J.S., Richardson, D.C., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.241 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

NADH oxidase /nitrite reductase from Pyrococcus furiosus Pfu-1140779-001

Horanyi, P., Tempel, W., Weinberg, M.V., Liu, Z.-J., Shah, A., Chen, L., Lee, D., SUGAR, F.J., BRERETON, P.S., IZUMI, M., POOLE II, F.L., SHAH, C., Jenney Jr., F.E., Arendall III, W.B., Rose, J.P., ADAMS, M.W.W., Richardson, J.S., Richardson, D.C., Wang, B.-C., Southeast Collaboratory for Structural Genomics

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.69 kDa 
• Atom Count: 2,725 
• Modeled Residue Count: 346 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH oxidase /nitrite reductase	A	367	Pyrococcus furiosus DSM 3638	Mutation(s): 0  EC: 1.18.1.4
UniProt
Find proteins for Q8U1K9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1K9  Go to UniProtKB:  Q8U1K9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.241 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.335	α = 90
b = 73.737	β = 90
c = 95.849	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-23 
Deposition Author(s): Horanyi, P., Tempel, W., Weinberg, M.V., Liu, Z.-J., Shah, A., Chen, L., Lee, D., Sugar, F.J., Brereton, P.S., Izumi, M., Poole II, F.L., Shah, C., Jenney Jr., F.E., Arendall III, W.B., Rose, J.P., Adams, M.W.W., Richardson, J.S., Richardson, D.C., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2004-11-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description