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- PDB-1ho1: CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1ho1
TitleCRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE
ComponentsPYRIDOXINE 5'-PHOSPHATE SYNTHASE
KeywordsBIOSYNTHETIC PROTEIN / TIM barrel
Function / homology
Function and homology information


pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / identical protein binding / cytosol
Similarity search - Function
Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ / Pyridoxine 5'-phosphate synthase / Pyridoxal phosphate biosynthesis protein PdxJ / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Pyridoxine 5'-phosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsGarrido-Franco, M. / Laber, B. / Huber, R. / Clausen, T.
CitationJournal: Structure / Year: 2001
Title: Structural basis for the function of pyridoxine 5'-phosphate synthase.
Authors: Franco, M.G. / Laber, B. / Huber, R. / Clausen, T.
History
DepositionDec 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
B: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
C: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
D: PYRIDOXINE 5'-PHOSPHATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)105,1614
Polymers105,1614
Non-polymers00
Water13,457747
1
A: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
B: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
C: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
D: PYRIDOXINE 5'-PHOSPHATE SYNTHASE

A: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
B: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
C: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
D: PYRIDOXINE 5'-PHOSPHATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)210,3218
Polymers210,3218
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)131.129, 155.358, 129.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is an octamer generated from the tetramer in the asymmetric unit by the operations: x,-y,-z

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Components

#1: Protein
PYRIDOXINE 5'-PHOSPHATE SYNTHASE / PYRIDOXAL PHOSPHATE BIOSYNTHETIC PROTEIN PDXJ


Mass: 26290.143 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PDXJ / Plasmid: PASK-IBA3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P0A794
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 3.15 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG6000, 2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
22 mMTris-HCl1drop
310 %PEG60001reservoir
42 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 16, 1999
RadiationMonochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 87995 / Num. obs: 345047 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.8 / Num. unique all: 48550 / Rsym value: 0.452 / % possible all: 98.5
Reflection
*PLUS
Num. obs: 87995 / Num. measured all: 345047
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2→20 Å / Isotropic thermal model: Anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorSelection details
Rfree0.253 random
Rwork0.206 -
all0.208 -
obs0.208 -
Displacement parametersBiso mean: 39.7 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7190 0 0 747 7937
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_mcbond_it3.09

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