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- PDB-8qyt: Human Pyridoxine-5'-phosphate oxidase in complex with PLP -

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Basic information

Entry
Database: PDB / ID: 8qyt
TitleHuman Pyridoxine-5'-phosphate oxidase in complex with PLP
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 / mitochondrion / 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
BETA-MERCAPTOETHANOL / FLAVIN MONONUCLEOTIDE / PYRIDOXAL-5'-PHOSPHATE / Pyridoxine-5'-phosphate oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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)31,1165
Polymers30,3111
Non-polymers8054
Water2,486138
1
A: Pyridoxine-5'-phosphate oxidase
hetero molecules

A: Pyridoxine-5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,23210
Polymers60,6232
Non-polymers1,6098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8960 Å2
ΔGint-52 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.480, 82.480, 59.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pyridoxine-5'-phosphate oxidase


Mass: 30311.295 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

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Non-polymers , 5 types, 142 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12% vv PEG 6000, 0.1M Sodium Citrate, 0.1M Lithium Sulfate

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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: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→45.6 Å / Num. obs: 26324 / % possible obs: 100 % / Redundancy: 18.4 % / CC1/2: 1 / Rrim(I) all: 0.05 / Net I/σ(I): 30.2
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 18.8 % / Rmerge(I) obs: 1.443 / Num. unique obs: 1316 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→45.6 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.226 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21563 1326 5 %RANDOM
Rwork0.17285 ---
obs0.17505 24998 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.046 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.16 Å2-0 Å2
2---0.31 Å20 Å2
3---1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.69→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 52 138 1904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131916
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171745
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.6592604
X-RAY DIFFRACTIONr_angle_other_deg1.3751.5834035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0495230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79321.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96215325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7811518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
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_it2.8163.292875
X-RAY DIFFRACTIONr_mcbond_other2.8033.292874
X-RAY DIFFRACTIONr_mcangle_it3.6874.9161096
X-RAY DIFFRACTIONr_mcangle_other3.694.9161097
X-RAY DIFFRACTIONr_scbond_it4.0393.7071041
X-RAY DIFFRACTIONr_scbond_other4.0443.7081038
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8585.4021501
X-RAY DIFFRACTIONr_long_range_B_refined7.21237.612138
X-RAY DIFFRACTIONr_long_range_B_other7.22737.2892112
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.691→1.735 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 96 -
Rwork0.234 1831 -
obs--100 %

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