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- PDB-3hy8: Crystal Structure of Human Pyridoxine 5'-Phosphate Oxidase R229W ... -

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Basic information

Entry
Database: PDB / ID: 3hy8
TitleCrystal Structure of Human Pyridoxine 5'-Phosphate Oxidase R229W Mutant
ComponentsPyridoxine-5'-phosphate oxidase
KeywordsOXIDOREDUCTASE / FMN binding protein / oxidase / Disease mutation / Epilepsy / Flavoprotein / FMN / Phosphoprotein / Pyridoxal phosphate / Pyridoxine biosynthesis
Function / homology
Function and homology information


pyridoxamine metabolic process / pyridoxal 5'-phosphate synthase / Vitamin B6 activation to pyridoxal phosphate / pyridoxamine phosphate oxidase activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / pyridoxal phosphate binding / FMN binding / protein homodimerization activity / cytosol
Similarity search - Function
Pyridoxamine 5'-phosphate oxidase, conserved site / Pyridoxamine 5'-phosphate oxidase signature. / Pyridoxine 5'-phosphate oxidase, dimerisation, C-terminal / Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region / Pyridoxamine 5'-phosphate oxidase / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel ...Pyridoxamine 5'-phosphate oxidase, conserved site / Pyridoxamine 5'-phosphate oxidase signature. / Pyridoxine 5'-phosphate oxidase, dimerisation, C-terminal / Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region / Pyridoxamine 5'-phosphate oxidase / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Pyridoxine-5'-phosphate oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsSafo, M.K. / Musayev, F.N. / Di Salvo, M.L. / Saavedra, M.K. / Schirch, V.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Molecular basis of reduced pyridoxine 5'-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder
Authors: Musayev, F.N. / Di Salvo, M.L. / Saavedra, M.A. / Contestabile, R. / Ghatge, M.S. / Haynes, A. / Schirch, V. / Safo, M.K.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxine-5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0466
Polymers30,0581
Non-polymers9885
Water90150
1
A: Pyridoxine-5'-phosphate oxidase
hetero molecules

A: Pyridoxine-5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,09312
Polymers60,1162
Non-polymers1,97710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area9420 Å2
ΔGint-81 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.270, 82.270, 58.788
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Pyridoxine-5'-phosphate oxidase / Pyridoxamine-phosphate oxidase


Mass: 30058.041 Da / Num. of mol.: 1 / Mutation: R229W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNPO / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(lambdaDE3)pLysS
References: UniProt: Q9NVS9, pyridoxal 5'-phosphate synthase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.91 Å3/Da / Density % sol: 35.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: mono-ammonium dihydrogen phosphate, Sodium Citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 23, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→35.63 Å / Num. obs: 8215 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.66 % / Biso Wilson estimate: 62.1 Å2 / Rmerge(I) obs: 0.056 / Χ2: 0.92 / Net I/σ(I): 22.5 / Scaling rejects: 7613
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 9.79 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 6.5 / Num. measured all: 8447 / Num. unique all: 800 / Χ2: 0.98 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
CNS1refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB Entry 1NRG

1nrg


Resolution: 2.5→22.02 Å / Rfactor Rfree error: 0.015 / Occupancy max: 1 / Occupancy min: 0.7 / Data cutoff high absF: 1931652 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 382 4.7 %RANDOM
Rwork0.226 ---
all0.229 8195 --
obs0.229 8195 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.775 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 99.62 Å2 / Biso mean: 61.287 Å2 / Biso min: 26.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å28.31 Å20 Å2
2--0.31 Å20 Å2
3----0.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→22.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 62 50 1844
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it5.451.5
X-RAY DIFFRACTIONc_mcangle_it7.382
X-RAY DIFFRACTIONc_scbond_it7.32
X-RAY DIFFRACTIONc_scangle_it9.292.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.399 54 5.4 %
Rwork0.324 946 -
all-1000 -
obs-1000 100 %

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