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Yorodumi- PDB-1bt4: PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS SUBSP. ALK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bt4 | ||||||
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Title | PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS SUBSP. ALKALOPHILUS | ||||||
Components | Phosphoserine aminotransferase | ||||||
Keywords | TRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / PHOSPHOSERINE / ALKALIPHILIC | ||||||
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 circulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hester, G. / Luong, T.N. / Moser, M. / Jansonius, J.N. | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of Phosphoserine Aminotransferase from Bacillus Circulans Subsp. Alkalophilus Authors: Hester, G. / Luong, T.N. / Moser, M. / Jansonius, J.N. #1: Journal: Protein Sci. / Year: 1996 Title: Crystallization and Preliminary X-Ray Analysis of Phosphoserine Aminotransferase from Bacillus Circulans Subsp. Alkalophilus Authors: Moser, M. / Muller, R. / Battchikova, N. / Koivulehto, M. / Korpela, T. / Jansonius, J.N. #2: Journal: Biochim.Biophys.Acta / Year: 1996 Title: Phosphoserine Aminotransferase from Bacillus Circulans Subsp. Alkalophilus: Purification, Gene Cloning and Sequencing Authors: Battchikova, N. / Himanen, J.-P. / Ahjolahti, M. / Korpela, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bt4.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bt4.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bt4_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 1bt4_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | 1bt4_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 1bt4_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/1bt4 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/1bt4 | HTTPS FTP |
-Related structure data
Related structure data | 1bjnS S: Starting model for refinement |
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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
#1: Protein | Mass: 39834.895 Da / Num. of mol.: 1 / Fragment: ONE COMPLETE SUBUNIT / Mutation: K3E / Source method: isolated from a natural source Details: THE COFACTOR PYRIDOXAL-5'-PHOSPHATE IS COVALENTLY LINKED TO THE SIDE CHAIN OF LYS 197 Source: (natural) Bacillus circulans (bacteria) / Variant: ALKALOPHILUS / Strain: subsp. alkalophilus / References: UniProt: Q59196, phosphoserine transaminase | ||
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#2: Chemical | ChemComp-PLP / | ||
#3: Water | ChemComp-HOH / | ||
Nonpolymer details | PLP MOLECULE IS COVALENTLYSequence details | MET 1 IS CLEAVED OFF IN A POST-TRANSLATIO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 48 % |
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Crystal grow | Method: macroseeding / pH: 4.6 Details: CRYSTALLIZED AT ROOM TEMPERATURE FROM 0.1 M SODIUM ACETATE BUFFER, PH 4.6, 2-6% GLYCEROL, 2-4% PEG 20000, USING MACROSEEDING TECHNIQUES, macroseeding Temp details: room temp |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1996 |
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→29.3 Å / Num. obs: 16466 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 5 / Rsym value: 0.219 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BJN Resolution: 2.3→29.3 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.35 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 15
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Xplor file |
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