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- PDB-1jnw: Active Site Structure of E. coli pyridoxine 5'-phosphate Oxidase -

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Basic information

Entry
Database: PDB / ID: 1jnw
TitleActive Site Structure of E. coli pyridoxine 5'-phosphate Oxidase
ComponentsPyridoxine 5'-phosphate oxidase
KeywordsOXIDOREDUCTASE / n-terminal segment / PLP / FMN
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 / PYRIDOXAL-5'-PHOSPHATE / 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: 2.07 Å
Authorsdi Salvo, M.L. / Ko, T.P. / Musayev, F.N. / Raboni, S. / Schirch, V. / Safo, M.K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Active site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase.
Authors: di Salvo, M.L. / Ko, T.P. / Musayev, F.N. / Raboni, S. / Schirch, V. / Safo, M.K.
History
DepositionJul 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)26,6184
Polymers25,8201
Non-polymers7983
Water4,810267
1
A: Pyridoxine 5'-phosphate oxidase
hetero molecules

A: Pyridoxine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2368
Polymers51,6392
Non-polymers1,5976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11140 Å2
ΔGint-37 kcal/mol
Surface area17850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.358, 52.238, 53.913
Angle α, β, γ (deg.)90.00, 101.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-302-

HOH

31A-303-

HOH

DetailsThe enzyme is a dimer, which can be generated by applying the crystallographic dyad symmetry to the monomer asymmetric unit.

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Components

#1: Protein Pyridoxine 5'-phosphate oxidase


Mass: 25819.666 Da / Num. of mol.: 1
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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: potassium phosphate, ammonium phosphate, mercaptoethanol, N-morpholinoethanesulfonate, dioxane, pyridoxal 5-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.3 mg/mlprotein1drop
2100 mMpotassium phosphate1droppH7.5
35 mM2-mercaptoethanol1drop
413 mMPLP1drop
51 Mammonium sulfate1reservoir
61.5 %(v/v)dioxane1reservoir
70.1 MMES-NaOH1reservoirpH7..0

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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: Dec 4, 2000 / Details: mirrors
RadiationMonochromator: OSMIC confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→44 Å / Num. all: 13991 / Num. obs: 13510 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.3
Reflection shellResolution: 2.07→2.14 Å / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.1 / % possible all: 92.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
bioteXdata reduction
bioteXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1dnl with omission of all waters, ligands and ions

1dnl


Resolution: 2.07→44.01 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 5761739.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 684 5.1 %RANDOM
Rwork0.178 ---
all0.182 13510 --
obs0.178 13510 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.7459 Å2 / ksol: 0.365904 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å2-0.27 Å2
2--8.07 Å20 Å2
3----5.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.21 Å
Luzzati d res low-6 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.07→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 52 267 2094
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.452.5
LS refinement shellResolution: 2.07→2.14 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.35 60 4.6 %
Rwork0.293 1244 -
obs-1403 92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4FMN.PARAMFMN.TOP
X-RAY DIFFRACTION5PLP.PARAMPLP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.45
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scangle_it2.452.5
LS refinement shell
*PLUS
Lowest resolution: 2.15 Å / Rfactor Rfree: 0.349 / % reflection Rfree: 4.6 %

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