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Yorodumi- PDB-4add: Structural and functional study of succinyl-ornithine transaminas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4add | ||||||
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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: 2.45 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 | 4add.cif.gz | 315.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4add.ent.gz | 259.2 KB | Display | PDB format |
PDBx/mmJSON format | 4add.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4add ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4add | HTTPS FTP |
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-Related 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 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21 References: UniProt: P77581, succinyldiaminopimelate transaminase, succinylornithine transaminase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-SUO / #4: Water | ChemComp-HOH / | Nonpolymer details | SUCCINYLOR | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.2 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 9 Details: 1.5 M AMMONIUM SULFATE, 10% (V/V) MMT (MALATE-MES-TRIS) BUFFER AT PH 9.0, 293K, 150 PLUS 150 NL DROPS. PROTEIN HAD PLP AND SUCCINYLORNITHINE PREVIOUSLY ADDED. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→19.8 Å / Num. obs: 85143 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREVIOUSLY-DETERMINED NATIVE Resolution: 2.45→108.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.609 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN TH INPUT. U VALUES REFINED INDIVIDUALLY. THERE IS A SMALL AMOUNT OF POSITIVE ELECTRON DENSITY THAT COULD NOT BE MODELLED WELL.
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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: 28.142 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→108.46 Å
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Refine LS restraints |
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