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- PDB-4adb: Structural and functional study of succinyl-ornithine transaminas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4adb | ||||||
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Title | Structural and functional study of succinyl-ornithine transaminase from E. coli | ||||||
![]() | SUCCINYLORNITHINE TRANSAMINASE | ||||||
![]() | TRANSFERASE / PLP ENZYMES / AMINOTRANSFERASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J. / Peat, T.S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.2 KB | Display | ![]() |
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PDB format | ![]() | 264.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.8 KB | Display | ![]() |
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Full document | ![]() | 504.1 KB | Display | |
Data in XML | ![]() | 66.2 KB | Display | |
Data in CIF | ![]() | 92.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4adcC ![]() 4addC ![]() 4adeC ![]() 2pb2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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) ![]() ![]() References: UniProt: P77581, succinyldiaminopimelate transaminase, succinylornithine transaminase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-NA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.6 % / 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 IN 150 PLUS 150 NL DROPS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / 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: 2.2→19.8 Å / Num. obs: 118526 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.4 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PB2 Resolution: 2.2→109.05 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.688 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.167 / 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 |
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Refinement step | Cycle: LAST / Resolution: 2.2→109.05 Å
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Refine LS restraints |
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