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- PDB-6h00: Crystal structure of human pyridoxine 5-phophate oxidase, R116Q v... -

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Basic information

Entry
Database: PDB / ID: 6h00
TitleCrystal structure of human pyridoxine 5-phophate oxidase, R116Q variant
ComponentsPyridoxine-5'-phosphate oxidase
KeywordsOXIDOREDUCTASE / PNPO / FMN-binding / PNP-oxidase activity
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 / Pyridoxine-5'-phosphate oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsMackinnon, S. / Wilson, M.P. / Shrestha, L. / Bezerra, G.A. / Newman, J. / Fox, N. / Sorrell, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. ...Mackinnon, S. / Wilson, M.P. / Shrestha, L. / Bezerra, G.A. / Newman, J. / Fox, N. / Sorrell, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Clayton, P.T. / Mills, P.B. / Yue, W.W.
CitationJournal: To Be Published
Title: Crystal structure of human pyridoxine 5-phophate oxidase, R116Q variant
Authors: Mackinnon, S. / Wilson, M.P. / Shrestha, L. / Bezerra, G.A. / Newman, J. / Fox, N. / Sorrell, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Clayton, P.T. / Mills, P.B. / Yue, W.W.
History
DepositionJul 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / reflns
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _reflns.number_obs

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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)30,9939
Polymers30,0001
Non-polymers9938
Water81145
1
A: Pyridoxine-5'-phosphate oxidase
hetero molecules

A: Pyridoxine-5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,98618
Polymers60,0002
Non-polymers1,98616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area9700 Å2
ΔGint-90 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.330, 83.330, 58.930
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: 29999.959 Da / Num. of mol.: 1 / Mutation: R116Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNPO / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NVS9, pyridoxal 5'-phosphate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% PEG1000, 0.2 M lithium sulphate, 0.1 M citrate, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.66→34.03 Å / Num. obs: 29800 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.02 / Rrim(I) all: 0.042 / Net I/σ(I): 17.9 / Num. measured all: 116657 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.66-1.74.21.053874420870.5140.5781.2071.499.8
7.42-34.033.60.03712443450.9970.0220.04347.995.3

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NRG

1nrg


Resolution: 1.66→34.03 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.601 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.084
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 1418 4.8 %RANDOM
Rwork0.169 ---
obs0.1705 28380 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.92 Å2 / Biso mean: 39.03 Å2 / Biso min: 21.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å2-0 Å2
2---0.18 Å20 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 1.66→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 62 45 1736
Biso mean--55.93 43.03 -
Num. residues----204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191760
X-RAY DIFFRACTIONr_bond_other_d0.0020.021585
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9872390
X-RAY DIFFRACTIONr_angle_other_deg0.94433651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8825210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0923.90887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0515279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5611513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211985
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02416
X-RAY DIFFRACTIONr_rigid_bond_restr2.21633345
X-RAY DIFFRACTIONr_sphericity_free26.553517
X-RAY DIFFRACTIONr_sphericity_bonded9.95753330
LS refinement shellResolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 119 -
Rwork0.24 2077 -
all-2196 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -26.6633 Å / Origin y: -6.6947 Å / Origin z: -2.038 Å
111213212223313233
T0.0228 Å2-0.0118 Å2-0.005 Å2-0.0204 Å2-0.009 Å2--0.0112 Å2
L0.5006 °2-0.0098 °20.1407 °2-2.0651 °2-0.0575 °2--1.3373 °2
S0.0289 Å °-0.0309 Å °0.0063 Å °0.1944 Å °-0.0831 Å °-0.0699 Å °0.0611 Å °-0.081 Å °0.0542 Å °

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