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- PDB-1npx: STRUCTURE OF NADH PEROXIDASE FROM STREPTOCOCCUS FAECALIS 10C1 REF... -

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Basic information

Entry
Database: PDB / ID: 1npx
TitleSTRUCTURE OF NADH PEROXIDASE FROM STREPTOCOCCUS FAECALIS 10C1 REFINED AT 2.16 ANGSTROMS RESOLUTION
ComponentsNADH PEROXIDASE
KeywordsOXIDOREDUCTASE(H2O2(A))
Function / homology
Function and homology information


NADH peroxidase / NADH peroxidase activity
Similarity search - Function
: / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain ...: / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADH peroxidase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.16 Å
AuthorsStehle, T. / Ahmed, S.A. / Claiborne, A. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Structure of NADH peroxidase from Streptococcus faecalis 10C1 refined at 2.16 A resolution.
Authors: Stehle, T. / Ahmed, S.A. / Claiborne, A. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Cloning, Sequence and Overexpression of Nadh Peroxidase from Streptococcus Faecalis 10C1. Structural Relationship with the Flavoprotein Disulfide Reductases
Authors: Ross, R.P. / Claiborne, A.
#2: Journal: FEBS Lett. / Year: 1990
Title: The Structure of Nadh Peroxidase from Streptococcus Faecalis at 3.3 Angstroms Resolution
Authors: Stehle, T. / Ahmed, S.A. / Claiborne, A. / Schulz, G.E.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: The Non-Flavin Redox Center of the Streptococcal Nadh Peroxidase. II. Evidence for a Stabilized Cysteine-Sulfenic Acid
Authors: Poole, L.B. / Claiborne, A.
#4: Journal: J.Biol.Chem. / Year: 1989
Title: The Non-Flavin Redox Center of the Streptococcal Nadh Peroxidase. I. Thiol Reactivity and Redox Behavior in the Presence of Urea
Authors: Poole, L.B. / Claiborne, A.
#5: Journal: J.Biol.Chem. / Year: 1986
Title: Interactions of Pyridine Nucleotides with Redox Forms of the Flavin-Containing Nadh Peroxidase from Streptococcus Faecalis
Authors: Poole, L.B. / Claiborne, A.
History
DepositionAug 2, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4372
Polymers49,6511
Non-polymers7861
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NADH PEROXIDASE
hetero molecules

A: NADH PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8744
Polymers99,3022
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8900 Å2
ΔGint-45 kcal/mol
Surface area33060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.200, 134.500, 145.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: RESIDUE CYS 42 IS A SULFONIC ACID (CYS42-SO3H).
2: DISCRETE DISORDER IS OBSERVED FOR SOME SIDE-CHAINS ATOMS OF RESIDUES ASP 25, LYS 51, ASP 124, AND ARG 447.
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

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Components

#1: Protein NADH PEROXIDASE


Mass: 49651.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / References: UniProt: P37062, NADH peroxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.77 %
Crystal grow
*PLUS
Temperature: 20-24 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
30.5 mMEDTA1drop
42 mMdithiothreitol1drop
60.5 mMEDTA1reservoir
72 mMdithiothreitol1reservoir
82.05 Mammonium sulfate1reservoir
90.005 mMFAD1reservoir
2potasssium phosphate1drop
5potasssium phosphate1reservoir
103 mM1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.16 Å / Lowest resolution: 9999 Å / Num. obs: 37857 / % possible obs: 92 % / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Highest resolution: 2.16 Å / Lowest resolution: 2.2 Å / % possible obs: 77 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.16→7 Å / Rfactor Rwork: 0.177 / Rfactor obs: 0.177 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.16→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 53 369 3915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.16 Å / Lowest resolution: 7 Å / Num. reflection all: 36563 / σ(F): 0 / Rfactor all: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_deg1.1

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