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- PDB-1nrg: Structure and Properties of Recombinant Human Pyridoxine-5'-Phosp... -

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Basic information

Entry
Database: PDB / ID: 1nrg
TitleStructure and Properties of Recombinant Human Pyridoxine-5'-Phosphate Oxidase
Componentspyridoxine 5'-phosphate oxidase
KeywordsOXIDOREDUCTASE / PLP / FMN / pyridoxine-5'-phosphate / oxidase
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
BETA-MERCAPTOETHANOL / FLAVIN MONONUCLEOTIDE / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Pyridoxine-5'-phosphate oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMusayev, F.N. / di Salvo, M.L. / Ko, T.P. / Schirch, V. / Safo, M.K.
CitationJournal: Protein Sci. / Year: 2003
Title: Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase.
Authors: Musayev, F.N. / Di Salvo, M.L. / Ko, T.P. / Schirch, V. / Safo, M.K.
History
DepositionJan 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_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: pyridoxine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9065
Polymers30,0291
Non-polymers8774
Water3,531196
1
A: pyridoxine 5'-phosphate oxidase
hetero molecules

A: pyridoxine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,81110
Polymers60,0582
Non-polymers1,7538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8750 Å2
ΔGint-51 kcal/mol
Surface area19270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.747, 82.747, 59.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer, which can be constructed from chain A and its symmetry-related partner generated by X-Y, -Y, 2/3-Z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein pyridoxine 5'-phosphate oxidase


Mass: 30029.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Human / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q9NVS9

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / 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: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.1 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: potassium/sodium tartarate, potassium phosphate, 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.35 Mpotassium sodium tartrate tetrahydrate1drop
34.2 mMPLP1drop
42.5 mM2-mercaptoethanol1drop
550 mMpotassium phosphate1droppH7.5
60.7 Mpotassium sodium tartrate tetrahydrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 16, 2002 / Details: mirrors
RadiationMonochromator: MSC Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→71.7 Å / Num. all: 17885 / Num. obs: 16966 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.59 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.0654 / Net I/σ(I): 14.7
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 1.63 / Num. unique all: 1226 / % possible all: 95.8
Reflection
*PLUS
Lowest resolution: 71 Å / Num. measured all: 94811 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 95.8 % / Num. unique obs: 1226 / Num. measured obs: 4746

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Processing

Software
NameVersionClassification
CNS1refinement
bioteXdata reduction
bioteXdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: E. coli PNPOx structure, PDB code 1G79

1g79


Resolution: 1.95→45.7 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 856 5 %RANDOM
Rwork0.192 ---
all0.201 17477 --
obs0.192 16953 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.1042 Å2 / ksol: 0.35217 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å21.73 Å20 Å2
2---1.49 Å20 Å2
3---2.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.95→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 56 196 1984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it5.161.5
X-RAY DIFFRACTIONc_mcangle_it6.062
X-RAY DIFFRACTIONc_scbond_it7.332
X-RAY DIFFRACTIONc_scangle_it9.222.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 156 5.6 %
Rwork0.297 2634 -
obs-2790 96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PHOSPHATE.PARWATER.TOP
X-RAY DIFFRACTION3FMN.PARFMN.TOP
X-RAY DIFFRACTION4PLP.PARPROTEIN.LINK
X-RAY DIFFRACTION5SEO2.PARPLP.TOP
Refinement
*PLUS
Lowest resolution: 45.7 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
LS refinement shell
*PLUS
Lowest resolution: 1.99 Å / Rfactor Rfree: 0.321 / Rfactor Rwork: 0.311 / Num. reflection obs: 1094

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