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- PDB-1ixq: Enzyme-Phosphate2 Complex of Pyridoxine 5'-Phosphate synthase -

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Basic information

Entry
Database: PDB / ID: 1ixq
TitleEnzyme-Phosphate2 Complex of Pyridoxine 5'-Phosphate synthase
ComponentsPyridoxine 5'-phosphate Synthase
KeywordsBIOSYNTHETIC PROTEIN / TIM barrel / enzyme-ligand complex / open-closed transition
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
PHOSPHATE ION / Pyridoxine 5'-phosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.3 Å
AuthorsGarrido-Franco, M. / Laber, B. / Huber, R. / Clausen, T.
Citation
Journal: J.MOL.BIOL. / Year: 2002
Title: Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis
Authors: Garrido-Franco, M. / Laber, B. / Huber, R. / Clausen, T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 5'-phosphate synthesizing enzyme
Authors: Garrido-Franco, M. / Huber, R. / Schmidt, F.S. / Laber, B. / Clausen, T.
#2: Journal: Structure / Year: 2001
Title: Structural Basis for the Function of Pyridoxine 5'-Phosphate Synthase
Authors: Garrido-Franco, M. / Laber, B. / Huber, R. / Clausen, T.
History
DepositionJun 28, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5408
Polymers105,1614
Non-polymers3804
Water5,999333
1
A: Pyridoxine 5'-phosphate Synthase
B: Pyridoxine 5'-phosphate Synthase
C: Pyridoxine 5'-phosphate Synthase
D: Pyridoxine 5'-phosphate Synthase
hetero molecules

A: Pyridoxine 5'-phosphate Synthase
B: Pyridoxine 5'-phosphate Synthase
C: Pyridoxine 5'-phosphate Synthase
D: Pyridoxine 5'-phosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,08116
Polymers210,3218
Non-polymers7608
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
2
B: Pyridoxine 5'-phosphate Synthase
hetero molecules

C: Pyridoxine 5'-phosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7704
Polymers52,5802
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2690 Å2
ΔGint-31 kcal/mol
Surface area18620 Å2
MethodPISA
3
D: Pyridoxine 5'-phosphate Synthase
hetero molecules

D: Pyridoxine 5'-phosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7704
Polymers52,5802
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2740 Å2
ΔGint-36 kcal/mol
Surface area18430 Å2
MethodPISA
4
A: Pyridoxine 5'-phosphate Synthase
hetero molecules

A: Pyridoxine 5'-phosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7704
Polymers52,5802
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2630 Å2
ΔGint-35 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.9, 155.4, 129.0
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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 3.12 Å3/Da / Density % sol: 60.56 %
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 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Details: microseeding, Garrido-Franco, M., (2000) Acta Crystallogr., Sect.D, 56, 1045.
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 198531 / Num. obs: 198531 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2
Reflection
*PLUS
Num. obs: 58001 / Num. measured all: 198531
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
SHARPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS
Starting model: native enzyme

Resolution: 2.3→20 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 2910 random
Rwork0.222 --
all0.224 58486 -
obs0.224 57991 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7096 0 20 333 7449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_bond_d0.009
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.46

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