1XHC

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), 0.270 (DCC)
R-Value Work:
0.200 (Depositor), 0.220 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U1K9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.241 (Depositor), 0.270 (DCC)
R-Value Work: 0.200 (Depositor), 0.220 (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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-11-23

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

Revision History (Full details and data files)

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