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Yorodumi- PDB-1r8k: PDXA PROTEIN; NAD-DEPENDENT DEHYDROGENASE/CARBOXYLASE; SUBUNIT OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r8k | ||||||
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Title | PDXA PROTEIN; NAD-DEPENDENT DEHYDROGENASE/CARBOXYLASE; SUBUNIT OF PYRIDOXINE PHOSPHATE BIOSYNTHETIC PROTEIN PDXJ-PDXA [SALMONELLA TYPHIMURIUM] | ||||||
Components | 4-hydroxythreonine-4-phosphate dehydrogenase 1 | ||||||
Keywords | OXIDOREDUCTASE / structural genomics / NAD-dependent dehydrogenase/carboxylase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information 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 / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Osipiuk, J. / Quartey, P. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: to be published Title: Crystal structure of NAD-dependent dehydrogenase/carboxylase of Salmonella typhimurium Authors: Osipiuk, J. / Quartey, P. / Moy, S. / Collart, F. / Joachimiak, A. #1: Journal: J.Biol.Chem. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r8k.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r8k.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 1r8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r8k_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
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Full document | 1r8k_full_validation.pdf.gz | 462.6 KB | Display | |
Data in XML | 1r8k_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 1r8k_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/1r8k ftp://data.pdbj.org/pub/pdb/validation_reports/r8/1r8k | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | putative biologically active dimer in asymmetric unit |
-Components
#1: Protein | Mass: 35140.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: PDXA, STM0090 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) References: UniProt: P58717, 4-hydroxythreonine-4-phosphate dehydrogenase #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MES buffer, Cobaltous Chloride, Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97919 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Oct 16, 2003 |
Radiation | Monochromator: double crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 46373 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 0.44 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→28.54 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2163601.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.0462 Å2 / ksol: 0.364881 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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