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- PDB-1ixo: Enzyme-analogue substrate complex of Pyridoxine 5'-Phosphate Synthase -

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Basic information

Entry
Database: PDB / ID: 1ixo
TitleEnzyme-analogue substrate 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
SN-GLYCEROL-3-PHOSPHATE / 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 1.3Nov 13, 2019Group: Data collection / Derived calculations / Category: reflns / struct_conn
Item: _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
Revision 1.6Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_symm_contact / struct_conn

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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)106,0219
Polymers105,1614
Non-polymers8605
Water5,909328
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)212,04218
Polymers210,3218
Non-polymers1,72110
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
2
C: Pyridoxine 5'-Phosphate synthase
hetero molecules

B: Pyridoxine 5'-Phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0975
Polymers52,5802
Non-polymers5163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3530 Å2
ΔGint-25 kcal/mol
Surface area18410 Å2
MethodPISA
3
A: Pyridoxine 5'-Phosphate synthase
hetero molecules

A: Pyridoxine 5'-Phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9244
Polymers52,5802
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3010 Å2
ΔGint-24 kcal/mol
Surface area18490 Å2
MethodPISA
4
D: Pyridoxine 5'-Phosphate synthase
hetero molecules

D: Pyridoxine 5'-Phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9244
Polymers52,5802
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3120 Å2
ΔGint-23 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.8, 155.9, 127.4
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-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H9O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.06 Å3/Da / Density % sol: 59.85 %
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: Aug 1, 2000
RadiationMonochromator: Si filter / Protocol: 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: 187532 / Num. obs: 187532 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05 / Rsym value: 0.5 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.7 / % possible all: 99.4
Reflection
*PLUS
Num. obs: 57133 / Num. measured all: 187532 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.22

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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 protein

Resolution: 2.3→20 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 2862 random
Rwork0.22 --
all0.223 57576 -
obs0.223 57123 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7096 0 50 328 7474
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_bond_d0.0086
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.009

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