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- PDB-1wv4: X-ray Structure of Escherichia coli pyridoxine 5'-phosphate oxida... -

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Basic information

Entry
Database: PDB / ID: 1wv4
TitleX-ray Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in tetragonal crystal form
ComponentsPyridoxamine 5'-phosphate oxidase
KeywordsOXIDOREDUCTASE / PLP / FMN / pyridoxal / pyridoxine 5'-phosphate / oxidase
Function / homology
Function and homology information


'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxal 5'-phosphate synthase / pyridoxamine phosphate oxidase activity / riboflavin binding / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / phosphate ion binding / pyridoxal phosphate binding / FMN binding / oxidoreductase activity ...'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxal 5'-phosphate synthase / pyridoxamine phosphate oxidase activity / riboflavin binding / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / phosphate ion binding / pyridoxal phosphate binding / FMN binding / oxidoreductase activity / protein homodimerization activity / protein-containing complex / 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 / PHOSPHATE ION / Pyridoxine/pyridoxamine 5'-phosphate oxidase / Pyridoxine/pyridoxamine 5'-phosphate oxidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSafo, M.K. / Musayev, F.N. / Schirch, V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme.
Authors: Safo, M.K. / Musayev, F.N. / Schirch, V.
History
DepositionDec 11, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Pyridoxamine 5'-phosphate oxidase
B: Pyridoxamine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2736
Polymers51,1702
Non-polymers1,1034
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-32 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.420, 54.420, 164.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Pyridoxamine 5'-phosphate oxidase / PNP/PMP oxidase / PNPOx


Mass: 25585.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET22b / Production host: Escherichia coli (E. coli)
References: UniProt: P28225, UniProt: P0AFI7*PLUS, pyridoxal 5'-phosphate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na Hepes, ammonium phosphate, potassium phosphate, mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Sep 27, 2000 / Details: mirrors
RadiationMonochromator: MSC Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→45.38 Å / Num. all: 14262 / Num. obs: 14262 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.4
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2819 / % possible all: 91.3

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Processing

Software
NameVersionClassification
CNS1refinement
bioteXdata reduction
bioteXdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DNL

1dnl


Resolution: 2.6→45.38 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 107804.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 709 5 %RANDOM
Rwork0.242 ---
all0.258 14262 --
obs0.242 14120 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.0777 Å2 / ksol: 0.342631 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å20 Å2
2---2.56 Å20 Å2
3---5.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.6→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 72 72 2773
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.26
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 109 4.7 %
Rwork0.292 2198 -
obs-2285 94.5 %

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