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Open data
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Basic information
Entry | Database: PDB / ID: 1ps7 | ||||||
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Title | Crystal structure of E.coli PdxA | ||||||
![]() | 4-hydroxythreonine-4-phosphate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / pyridoxine biosynthesis | ||||||
Function / homology | ![]() 4-hydroxythreonine-4-phosphate dehydrogenase / 4-hydroxythreonine-4-phosphate dehydrogenase activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / cobalt ion binding / NAD binding / magnesium ion binding / protein homodimerization activity / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sivaraman, J. / Li, Y. / Banks, J. / Cane, D.E. / Matte, A. / Cygler, M. | ||||||
![]() | ![]() Title: Crystal Structure of Escherichia coli PdxA, an Enzyme Involved in the Pyridoxal Phosphate Biosynthesis Pathway Authors: Sivaraman, J. / Li, Y. / Banks, J. / Cane, D.E. / Matte, A. / Cygler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.6 KB | Display | ![]() |
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PDB format | ![]() | 203.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Unit cell |
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Components
#1: Protein | Mass: 35477.914 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P19624, 4-hydroxythreonine-4-phosphate dehydrogenase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Citrate, MgCl2, PEG 8K, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 17, 2002 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.995 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 44107 / Num. obs: 44107 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.092 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.47→2.54 Å / % possible all: 63.5 |
Reflection | *PLUS Num. obs: 44115 / Num. measured all: 232767 / Rmerge(I) obs: 0.092 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PdxA native model Resolution: 2.47→45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.47→45 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.45 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |