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Yorodumi- PDB-4azj: Structural basis of L-phosphoserine binding to Bacillus alcalophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4azj | ||||||
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Title | Structural basis of L-phosphoserine binding to Bacillus alcalophilus phosphoserine aminotransferase | ||||||
Components | PHOSPHOSERINE AMINOTRANSFERASEPhosphoserine transaminase | ||||||
Keywords | TRANSFERASE | ||||||
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: 1.5 Å | ||||||
Authors | Battula, P. / Dubnovitsky, A.P. / Papageorgiou, A.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase Authors: Battula, P. / Dubnovitsky, A.P. / 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 | 4azj.cif.gz | 182 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4azj.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 4azj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/4azj ftp://data.pdbj.org/pub/pdb/validation_reports/az/4azj | HTTPS FTP |
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-Related structure data
Related structure data | 4azkC 1w23S 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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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: COVALENT BOND BETWEEN PLP AND L-PHOSPHOSERINE / 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 , 5 types, 1135 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 1.4 M TRI-SODIUM CITRATE, 0.1 M TRIS-HCL, PH 8.5. C0-CRYSTALLIZATION WITH 25 MM L-PHOSPHOSERINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.097 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 5, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.097 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 170566 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.5→1.54 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W23 Resolution: 1.5→19.876 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 14.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.489 Å2 / ksol: 0.422 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→19.876 Å
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Refine LS restraints |
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LS refinement shell |
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