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Yorodumi- PDB-1w23: Crystal structure of phosphoserine aminotransferase from Bacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w23 | ||||||
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Title | Crystal structure of phosphoserine aminotransferase from Bacillus alcalophilus | ||||||
Components | PHOSPHOSERINE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE | ||||||
Function / homology | Function and homology information phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / L-serine biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | BACILLUS ALCALOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å | ||||||
Authors | Dubnovitsky, A. / Kapetaniou, E.G. / Papageorgiou, A.C. | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: Enzyme Adaptation to Alkaline Ph: Atomic Resolution (1.08 A) Structure of Phosphoserine Aminotransferase from Bacillus Alcalophilus Authors: Dubnovitsky, A. / Kapetaniou, E.G. / Papageorgiou, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w23.cif.gz | 340.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w23.ent.gz | 277.6 KB | Display | PDB format |
PDBx/mmJSON format | 1w23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w23_validation.pdf.gz | 495.9 KB | Display | wwPDB validaton report |
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Full document | 1w23_full_validation.pdf.gz | 509.9 KB | Display | |
Data in XML | 1w23_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 1w23_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/1w23 ftp://data.pdbj.org/pub/pdb/validation_reports/w2/1w23 | HTTPS FTP |
-Related structure data
Related structure data | 1w3uC 1bjnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40243.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PYRIDOXAL-5'-PHOSPHATE LINKED TO 196 / Source: (gene. exp.) BACILLUS ALCALOPHILUS (bacteria) / Plasmid: PBALC-PSAT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RME2, phosphoserine transaminase |
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-Non-polymers , 8 types, 993 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PEG / | #4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Chemical | ChemComp-EPE / | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE N-TERMINAL METHIONINE |
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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: 2.19 Å3/Da / Density % sol: 43.8 % |
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Crystal grow | pH: 7.5 Details: 27.75% (V/V) PEG 400, 185 MM MAGNESIUM CHLORIDE HEXAHYDRATE, 7.5% (V/V) GLYCEROL AND 92.7 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9007 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 4, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9007 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→20 Å / Num. obs: 351228 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 23.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.9 |
Reflection shell | Resolution: 1.08→1.11 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BJN Resolution: 1.08→20 Å / Num. parameters: 62075 / Num. restraintsaints: 75657 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.03. RESIDUES A 215, A 216, A 218, A 219 AND B 218 WERE MODELLED AS ALANINES. RESIDUES B 214, B 215, B 216 WERE NOT MODELLED.
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Refine analyze | Num. disordered residues: 59 / Occupancy sum hydrogen: 4734 / Occupancy sum non hydrogen: 6669 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→20 Å
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Refine LS restraints |
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