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Yorodumi- PDB-4adc: Structural and functional study of succinyl-ornithine transaminas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4adc | ||||||
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Title | Structural and functional study of succinyl-ornithine transaminase from E. coli | ||||||
Components | SUCCINYLORNITHINE TRANSAMINASE | ||||||
Keywords | TRANSFERASE / PLP ENZYMES / AMINOTRANSFERASE | ||||||
Function / homology | Function and homology information succinylornithine transaminase / succinylornithine transaminase activity / ornithine catabolic process / arginine catabolic process to succinate / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / arginine catabolic process to glutamate / arginine biosynthetic process via ornithine / arginine catabolic process / pyridoxal phosphate binding / identical protein binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Newman, J. / Peat, T.S. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Determination of the Structure of the Catabolic N-Succinylornithine Transaminase (Astc) from Escherichia Coli. Authors: Newman, J. / Seabrook, S. / Surjadi, R. / Williams, C.C. / Lucent, D. / Wilding, M. / Scott, C. / Peat, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4adc.cif.gz | 319.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4adc.ent.gz | 260.7 KB | Display | PDB format |
PDBx/mmJSON format | 4adc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4adc ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4adc | HTTPS FTP |
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-Related structure data
Related structure data | 4adbC 4addC 4adeC 2pb2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43712.207 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: NATIVE FROM E. COLI / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21List of strains of Escherichia coli References: UniProt: P77581, succinylornithine transaminase, succinyldiaminopimelate transaminase #2: Chemical | ChemComp-PLP / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Nonpolymer details | PYRIDOXYL PHOSPHATE (PLP): PLP IS FREE FROM LYSINE 252 SCHIFF BASE | |
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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: 3.45 Å3/Da / Density % sol: 64.3 % / Description: NONE |
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Crystal grow | pH: 8 Details: 1.17 M SODIUM MALONATE PH 7.0, 0.09 M TRIS CHLORIDE PH 8.0, 0.02 M DI-ETHYLAMMONIUM FORMATE WITH DRY ORNITHINE POWDER ADDED DIRECTLY TO THE CRYSTAL DROPS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.8 Å / Num. obs: 101215 / % possible obs: 97.8 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PB2 Resolution: 2.3→108.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.582 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.519 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→108.69 Å
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Refine LS restraints |
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