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- PDB-1g77: X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5`-PHOSPHATE OXIDA... -

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Basic information

Entry
Database: PDB / ID: 1g77
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
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: 2.1 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_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
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)26,7135
Polymers25,8201
Non-polymers8934
Water1,76598
1
A: PYRIDOXINE 5`-PHOSPHATE OXIDASE
hetero molecules

A: PYRIDOXINE 5`-PHOSPHATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,42610
Polymers51,6392
Non-polymers1,7878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area9220 Å2
ΔGint-44 kcal/mol
Surface area17100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.440, 63.440, 124.640
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 was constructued from chain A and its symmetry partner generated by the two-fold axis

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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.: 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.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium formate 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 23, 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: 2.1→55 Å / Num. all: 17276 / Num. obs: 17276 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 5.6 / Net I/σ(I): 10.8
Reflection shellResolution: 2.1→2.33 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 3 / Num. unique all: 4480 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 63660
Reflection shell
*PLUS
% possible obs: 96.5 % / Num. possible: 14406 / Num. unique obs: 4480

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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: 2.1→55 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 53854.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh and Huber / Details: bulk solvent correction
RfactorNum. reflection% reflectionSelection details
Rfree0.236 872 5.2 %RANDOM
Rwork0.209 ---
all0.21493 17276 --
obs0.21008 16766 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.46 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å24.67 Å20 Å2
2--3.91 Å20 Å2
3----7.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 57 98 1797
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.362.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 143 5.5 %
Rwork0.265 2455 -
obs-2598 90.8 %
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 DIFFRACTION5&_1_PARAMETER_INFILE_6PLP.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_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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