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- PDB-1f8w: CRYSTAL STRUCTURE OF NADH PEROXIDASE MUTANT: R303M -

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Basic information

Entry
Database: PDB / ID: 1f8w
TitleCRYSTAL STRUCTURE OF NADH PEROXIDASE MUTANT: R303M
ComponentsNADH PEROXIDASE
KeywordsOXIDOREDUCTASE / Interface / FAD / NAD-binding domains
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 / SYNCHROTRON / Resolution: 2.45 Å
AuthorsYeh, J.I. / Claiborne, A. / Hol, W.G.J.
Citation
Journal: Biochemistry / Year: 2000
Title: Analysis of the kinetic and redox properties of the NADH peroxidase R303M mutant: correlation with the crystal structure.
Authors: Crane III, E.J. / Yeh, J.I. / Luba, J. / Claiborne, A.
#1: Journal: Biochemistry / Year: 1996
Title: Structure of the Native Cysteine-sulfenic Acid Redox Center of Enterococcal NADH Peroxidase Refined at 2.8 A Resolution
Authors: Yeh, J.I. / Claiborne, A. / Hol, W.G.
History
DepositionJul 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: NADH PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3792
Polymers49,5931
Non-polymers7861
Water2,360131
1
A: NADH PEROXIDASE
hetero molecules

A: NADH PEROXIDASE
hetero molecules

A: NADH PEROXIDASE
hetero molecules

A: NADH PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,5158
Polymers198,3734
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
2
A: NADH PEROXIDASE
hetero molecules

A: NADH PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7584
Polymers99,1862
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556y,x,-z+11
Buried area8960 Å2
ΔGint-54 kcal/mol
Surface area32580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)155.18, 155.18, 189.41
Angle α, β, γ (deg.)90, 90, 90
Int Tables number98
Space group name H-MI4122
DetailsFUNCTIONAL MOLECULE IS A HOMOTETRAMER

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Components

#1: Protein NADH PEROXIDASE


Mass: 49593.230 Da / Num. of mol.: 1 / Mutation: ARG 303 TO MET 303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: PR303M / Production host: Escherichia coli (E. coli) / 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.: 131 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 2% PEG 400, 2.0 M (NH4)2SO4, 100 mM Na Hepes, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-8 %PEG4001drop
21.6-1.9 Mammonium sulfate1drop
30.1 Msodium HEPES1drop
47.5-10 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 8, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.45→99 Å / Num. all: 42662 / Num. obs: 36615 / % possible obs: 85.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.5
Reflection shellHighest resolution: 2.45 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.39 / % possible all: 71.1
Reflection
*PLUS
Num. measured all: 60231 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Lowest resolution: 2.56 Å / % possible obs: 70.9 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.45→50 Å / Cross valid method: X-PLOR FreeR / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1821 5 %Random
Rwork0.196 ---
all0.281 36614 --
obs0.243 36614 86 %-
Refine analyzeLuzzati sigma a obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 53 131 3672
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg3
X-RAY DIFFRACTIONc_torsion_impr_deg1.07
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg3

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