1NPX | pdb_00001npx

STRUCTURE OF NADH PEROXIDASE FROM STREPTOCOCCUS FAECALIS 10C1 REFINED AT 2.16 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1NPX/pdb

• Classification: OXIDOREDUCTASE(H2O2(A))
• Organism(s): Enterococcus faecalis
• Mutation(s): No 


• Deposited: 1991-08-02 Released: 1994-01-31 
• Deposition Author(s): Stehle, T., Ahmed, S.A., Claiborne, A., Schulz, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Work: 
  0.177 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Structure of NADH peroxidase from Streptococcus faecalis 10C1 refined at 2.16 A resolution.

Stehle, T., Ahmed, S.A., Claiborne, A., Schulz, G.E.

(1991) J Mol Biology 221: 1325-1344

• PubMed: 1942054 
• Primary Citation Related Structures: 
  1NPX


• PubMed Abstract: 
  

  The crystal structure of NADH peroxidase (EC 1.11.1.1) from Streptococcus faecalis 10C1 (Enterococcus faecalis) has been refined to a resolution of 2.16 A using the simulated annealing method. The final crystallographic R-factor is 17.7% for all data in the resolution range 7 to 2.16 A. The standard deviations are 0.015 A in bond lengths and 3.0 degrees in bond angles for the final model, which includes all 447 amino acid residues, one FAD and 369 water molecules. The enzyme is a symmetrical tetramer with point group D2; the symmetry is crystallographic. The redox center of the enzyme consists of FAD and a cysteine (Cys42), which forms a sulfenic acid (Cys-SOH) in its oxidized state. A histidine (His10) close to Cys42 is likely to act as an active-site base. In the analyzed crystal, the enzyme was in a non-native oxidation state with Cys42 oxidized to a sulfonic acid Cys-SO3H. The chain fold of NADH peroxidase is similar to those of disulfide oxidoreductases. A comparison with glutathione reductase, a representative of this enzyme family, is given.

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Organizational Affiliation: 
• Institut für Organische Chemie und Biochemie der Universität, Freiburg, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 50.44 kDa 
• Atom Count: 3,915 
• Modeled Residue Count: 447 
• Deposited Residue Count: 447 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH PEROXIDASE	A	447	Enterococcus faecalis	Mutation(s): 0  EC: 1.11.1.1
UniProt
Find proteins for P37062 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore P37062  Go to UniProtKB:  P37062

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Work:  0.177 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.2	α = 90
b = 134.5	β = 90
c = 145.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Stehle, T., Ahmed, S.A., Claiborne, A., Schulz, G.E.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other