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- PDB-1ho4: CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1ho4
TitleCRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE IN COMPLEX WITH PYRIDOXINE 5'-PHOSPHATE AND INORGANIC PHOSPHATE
ComponentsPYRIDOXINE 5'-PHOSPHATE SYNTHASE
KeywordsBIOSYNTHETIC PROTEIN / TIM Barrel / Open-Closed Transition / Enzyme-Product Complex / Water Channel
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 / Pyridoxine 5'-phosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Derived calculations / 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 / 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)106,44211
Polymers105,1614
Non-polymers1,2827
Water13,241735
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)212,88422
Polymers210,3218
Non-polymers2,56314
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
2
A: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
hetero molecules

A: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2696
Polymers52,5802
Non-polymers6884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4120 Å2
ΔGint-42 kcal/mol
Surface area18870 Å2
MethodPISA
3
B: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
hetero molecules

C: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2696
Polymers52,5802
Non-polymers6884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4120 Å2
ΔGint-37 kcal/mol
Surface area18880 Å2
MethodPISA
4
D: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
hetero molecules

D: PYRIDOXINE 5'-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0794
Polymers52,5802
Non-polymers4982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3440 Å2
ΔGint-18 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.800, 156.300, 127.500
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.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PXP / PYRIDOXINE-5'-PHOSPHATE


Mass: 249.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H12NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 54860 / Num. obs: 110743 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.6 / Num. unique all: 13071 / Rsym value: 0.208 / % possible all: 95.7
Reflection
*PLUS
Num. obs: 54860 / Num. measured all: 110743
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HOI

1hoi


Resolution: 2.3→20 Å / Isotropic thermal model: Anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.245 2736 random
Rwork0.187 --
all0.195 54828 -
obs0.195 52092 -
Displacement parametersBiso mean: 56.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7334 0 79 735 8148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONn_bond_d0.011
X-RAY DIFFRACTIONc_mcbond_it2.33
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Type: c_bond_d

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