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Open data
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Basic information
Entry | Database: PDB / ID: 1ixq | ||||||
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Title | Enzyme-Phosphate2 Complex of Pyridoxine 5'-Phosphate synthase | ||||||
![]() | Pyridoxine 5'-phosphate Synthase | ||||||
![]() | BIOSYNTHETIC PROTEIN / TIM barrel / enzyme-ligand complex / open-closed transition | ||||||
Function / homology | ![]() pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Garrido-Franco, M. / Laber, B. / Huber, R. / Clausen, T. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: Structural Basis for the Function of Pyridoxine 5'-Phosphate Synthase Authors: Garrido-Franco, M. / Laber, B. / Huber, R. / Clausen, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.7 KB | Display | ![]() |
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PDB format | ![]() | 152.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.3 KB | Display | ![]() |
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Full document | ![]() | 501.9 KB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | The 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 | Mass: 26290.143 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.56 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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 dropDetails: microseeding, Garrido-Franco, M., (2000) Acta Crystallogr., Sect.D, 56, 1045. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: native enzyme Resolution: 2.3→20 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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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 |