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- PDB-1nhp: CRYSTALLOGRAPHIC ANALYSES OF NADH PEROXIDASE CYS42ALA AND CYS42SE... -

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Basic information

Entry
Database: PDB / ID: 1nhp
TitleCRYSTALLOGRAPHIC ANALYSES OF NADH PEROXIDASE CYS42ALA AND CYS42SER MUTANTS: ACTIVE SITE STRUCTURE, MECHANISTIC IMPLICATIONS, AND AN UNUSUAL ENVIRONMENT OF ARG303
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 Å
AuthorsMande, S.S. / Claiborne, A. / Hol, W.G.J.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystallographic analyses of NADH peroxidase Cys42Ala and Cys42Ser mutants: active site structures, mechanistic implications, and an unusual environment of Arg 303.
Authors: Mande, S.S. / Parsonage, D. / Claiborne, A. / Hol, W.G.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Structure of Nadh Peroxidase from Streptococcus Faecalis 10C1 Refined at 2.16 Angstroms
Authors: Stehle, T. / Ahmed, S.A. / Claiborne, A. / Schulz, G.E.
History
DepositionDec 9, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 28, 2012Group: Structure summary
Revision 1.4Feb 14, 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_ref_seq_dif / 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_ref_seq_dif.details / _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)50,5494
Polymers49,5711
Non-polymers9783
Water4,378243
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)101,0988
Polymers99,1422
Non-polymers1,9556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9870 Å2
ΔGint-105 kcal/mol
Surface area33160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.600, 134.800, 146.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsNADH PEROXIDASE IS A TETRAMER CONSISTING OF FOUR IDENTICAL SUBUNITS. THE SUBUNITS ARE RELATED THROUGH CRYSTALLOGRAPHIC SYMMETRY OPERATIONS.

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Components

#1: Protein NADH PEROXIDASE


Mass: 49571.164 Da / Num. of mol.: 1 / Mutation: C42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / References: UniProt: P37062, NADH peroxidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.86 Å3/Da / Density % sol: 68.11 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
225 mMpotassium phosphate1drop
30.3 mMEDTA1drop
42 mMdithiothreitol1drop
51.9 Mammonium sulfate1reservoir
60.005 mMFAD1reservoir
7100 mMpotassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 49100 / % possible obs: 90.6 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 2.04 Å / Lowest resolution: 2.09 Å / % possible obs: 74.2 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.176 -
obs0.176 46357
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 63 243 3795
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_dihedral_angle_deg1

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