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- PDB-1g79: X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDA... -

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Basic information

Entry
Database: PDB / ID: 1g79
TitleX-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION
ComponentsPYRIDOXINE 5'-PHOSPHATE OXIDASE
KeywordsOXIDOREDUCTASE / PLP complex / FMN complex / pyridoxine 5'-phosphate
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. / 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 / 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. / 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 / 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/pyridoxamine 5'-phosphate oxidase / Pyridoxine/pyridoxamine 5'-phosphate oxidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSafo, M.K. / Musayev, F.N. / di Salvo, M.L. / Schirch, V.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 2.0 A resolution.
Authors: Safo, M.K. / Musayev, F.N. / di Salvo, M.L. / Schirch, V.
History
DepositionNov 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2000Provider: 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 9, 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: PYRIDOXINE 5'-PHOSPHATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8047
Polymers25,5851
Non-polymers1,2196
Water2,594144
1
A: PYRIDOXINE 5'-PHOSPHATE OXIDASE
hetero molecules

A: PYRIDOXINE 5'-PHOSPHATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,60814
Polymers51,1702
Non-polymers2,43712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area9890 Å2
ΔGint-56 kcal/mol
Surface area17750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.720, 63.720, 124.360
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 constructued from chain A symmetry partner generated by the two-fold axis

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PYRIDOXINE 5'-PHOSPHATE OXIDASE


Mass: 25585.188 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

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Non-polymers , 5 types, 150 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / 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.: 2 / 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.: 144 / 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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate and MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.2 / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.8-1.1 Mammonium sulfate1reservoir
20.1 MMES-NaOH1reservoir
35 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 24, 2000 / Details: mirrors
RadiationMonochromator: MSC mirrors / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→55 Å / Num. all: 20202 / Num. obs: 20202 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.051 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2659 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 71938
Reflection shell
*PLUS
% possible obs: 97.7 % / Num. possible: 8521 / Num. unique obs: 2659

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Processing

Software
NameClassification
CNSrefinement
bioteXdata reduction
bioteXdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1DNL

1dnl


Resolution: 2→55 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 78166.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber / Details: bulk solvent correction
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1037 5.1 %RANDOM
Rwork0.208 ---
all0.2114 20197 --
obs0.2114 20197 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.73 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å23.14 Å20 Å2
2--3.9 Å20 Å2
3----7.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 77 144 1863
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 177 5.4 %
Rwork0.249 3111 -
obs-4288 98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAramPROTEIN.TOP
X-RAY DIFFRACTION2phosphate.paramWATER.TOP
X-RAY DIFFRACTION3fmn.paramFMN.TOP
X-RAY DIFFRACTION4plp.paramPHOSPHATE.TOP
X-RAY DIFFRACTION5seo.paramPLP.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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