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Yorodumi- PDB-8ht4: Crystal structure of Acetylornithine aminotransferase complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ht4 | ||||||
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Title | Crystal structure of Acetylornithine aminotransferase complex with PLP from Corynebacterium glutamicum | ||||||
Components | Acetylornithine aminotransferase | ||||||
Keywords | TRANSFERASE / Acetylornithine aminotransferase / Corynebacterium glutamicum | ||||||
Function / homology | Function and homology information acetylornithine transaminase / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / arginine biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Ki, D. / Kim, K.-J. | ||||||
Funding support | 1items
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Citation | Journal: J.Agric.Food Chem. / Year: 2023 Title: Crystal Structure and Functional Characterization of Acetylornithine Aminotransferase from Corynebacterium glutamicum. Authors: Ki, D. / Hong, H. / Kim, I.K. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ht4.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ht4.ent.gz | 124.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ht4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/8ht4 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/8ht4 | HTTPS FTP |
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-Related structure data
Related structure data | 8ht2SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42318.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Gene: argD, Cgl1397, cg1583 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59282, acetylornithine transaminase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 12% (W/V) PEG 3350, 8% Tacsimate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 7, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 24581 / % possible obs: 97.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.064 / Rrim(I) all: 0.166 / Χ2: 5.126 / Net I/σ(I): 11.7 / Num. measured all: 161300 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8HT2 Resolution: 2.51→32.51 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.87 / SU B: 11.018 / SU ML: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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 max: 81.58 Å2 / Biso mean: 23.216 Å2 / Biso min: 2.22 Å2
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Refinement step | Cycle: final / Resolution: 2.51→32.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.51→2.573 Å / Rfactor Rfree error: 0
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