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- PDB-8qyw: Human Pyridoxine-5'-phosphate oxidase mutant R225H -

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Basic information

Entry
Database: PDB / ID: 8qyw
TitleHuman Pyridoxine-5'-phosphate oxidase mutant R225H
ComponentsPyridoxine-5'-phosphate oxidase
KeywordsOXIDOREDUCTASE / Pyridoxine biosynthesis / Flavoprotein / Pyridoxal phosphate
Function / homology
Function and homology information


pyridoxal 5'-phosphate synthase / pyridoxamine metabolic process / 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. / Pyridoxamine 5'-phosphate oxidase / Pyridoxine 5'-phosphate oxidase, dimerisation, C-terminal / Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / FMN-binding split barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Pyridoxine-5'-phosphate oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.746 Å
AuthorsAntonelli, L. / Ilari, A. / Fiorillo, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: Identification of the pyridoxal 5'-phosphate allosteric site in human pyridox(am)ine 5'-phosphate oxidase.
Authors: Barile, A. / Graziani, C. / Antonelli, L. / Parroni, A. / Fiorillo, A. / di Salvo, M.L. / Ilari, A. / Giorgi, A. / Rosignoli, S. / Paiardini, A. / Contestabile, R. / Tramonti, A.
History
DepositionOct 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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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)31,1286
Polymers30,2921
Non-polymers8365
Water724
1
A: Pyridoxine-5'-phosphate oxidase
hetero molecules

A: Pyridoxine-5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,25712
Polymers60,5852
Non-polymers1,67210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8770 Å2
ΔGint-86 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.880, 82.880, 60.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 30292.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: We have reported the complete sequence but the discrepancies are due to the fact that the N-Terminal portion /1-45 residues) and the loop (residues 236 to 242) are highly mobile and ...Details: We have reported the complete sequence but the discrepancies are due to the fact that the N-Terminal portion /1-45 residues) and the loop (residues 236 to 242) are highly mobile and therefore we were not able to reconstruct these segments.
Source: (gene. exp.) Homo sapiens (human) / Gene: PNPO / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NVS9, pyridoxal 5'-phosphate synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1 M Ammonium Sulfate, 2% PEG400, 0.1 M HEPES pH 7.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.746→71.78 Å / Num. obs: 6519 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.999 / Net I/σ(I): 21.5
Reflection shellResolution: 2.747→2.792 Å / Num. unique obs: 323 / CC1/2: 0.866

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
autoPROCdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.746→41.47 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 15.464 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23894 343 5.3 %RANDOM
Rwork0.19836 ---
obs0.20054 6175 99.68 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.813 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å2-0.94 Å2-0 Å2
2---1.89 Å20 Å2
3---6.13 Å2
Refinement stepCycle: 1 / Resolution: 2.746→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 51 4 1764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0121806
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7271.6462448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3335206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91821.944108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73115300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7381514
X-RAY DIFFRACTIONr_chiral_restr0.0570.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021418
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3368.041830
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.89612.0561034
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6368.246974
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.027105.1252607
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.747→2.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 20 -
Rwork0.292 454 -
obs--99.79 %

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