+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ixn | ||||||
---|---|---|---|---|---|---|---|
Title | Enzyme-Substrate Complex of Pyridoxine 5'-Phosphate Synthase | ||||||
![]() | Pyridoxine 5'-Phosphate Synthase | ||||||
![]() | BIOSYNTHETIC PROTEIN / TIM barrel / enzyme-substrate 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 206.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 165.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is an octamer generated from the tetramer in the asymmetric unit by the operations: x,-y,-z |
-
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-DXP / #3: Chemical | ChemComp-G3P / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.74 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 2000 |
Radiation | Monochromator: Si filter / 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: 165177 / Num. obs: 165177 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1.6 / % possible all: 90.4 |
Reflection | *PLUS Num. obs: 53504 / % possible obs: 90.4 % / Num. measured all: 165177 |
Reflection shell | *PLUS % possible obs: 93.8 % |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: native protein Resolution: 2.3→20 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.18 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|