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Yorodumi- PDB-3it4: The Crystal Structure of Ornithine Acetyltransferase from Mycobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3it4 | ||||||
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Title | The Crystal Structure of Ornithine Acetyltransferase from Mycobacterium tuberculosis (Rv1653) at 1.7 A | ||||||
Components | (Arginine biosynthesis bifunctional protein argJ ...) x 2 | ||||||
Keywords | TRANSFERASE / Mycobacterium tuberculosis / Ornithine acetyltransferase / structural genomics / TB Structural Genomics Consortium (TBSGC) / Acyltransferase / Amino-acid biosynthesis / Arginine biosynthesis / Cytoplasm / Multifunctional enzyme | ||||||
Function / homology | Function and homology information glutamate N-acetyltransferase / glutamate N-acetyltransferase activity / ornithine biosynthetic process / methione N-acyltransferase activity / amino-acid N-acetyltransferase / acetyl-CoA:L-glutamate N-acetyltransferase activity / arginine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Sankaranarayanan, R. / Cherney, M.M. / Garen, C. / Garen, G. / Yuan, M. / James, M.N. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: The molecular structure of ornithine acetyltransferase from Mycobacterium tuberculosis bound to ornithine, a competitive inhibitor. Authors: Sankaranarayanan, R. / Cherney, M.M. / Garen, C. / Garen, G. / Niu, C. / Yuan, M. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3it4.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3it4.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 3it4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3it4_validation.pdf.gz | 483.9 KB | Display | wwPDB validaton report |
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Full document | 3it4_full_validation.pdf.gz | 487.8 KB | Display | |
Data in XML | 3it4_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 3it4_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/3it4 ftp://data.pdbj.org/pub/pdb/validation_reports/it/3it4 | HTTPS FTP |
-Related structure data
Related structure data | 3it6C 1vz6S 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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1 |
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Unit cell |
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-Components
-Arginine biosynthesis bifunctional protein argJ ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 19981.654 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: argJ, MT1691, MTCY06H11.18, Rv1653 / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli) References: UniProt: P63571, UniProt: P9WPZ3*PLUS, glutamate N-acetyltransferase #2: Protein | Mass: 21188.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: argJ, Rv1653, MT1691, MTCY06H11.18 / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli) References: UniProt: P63571, UniProt: P9WPZ3*PLUS, amino-acid N-acetyltransferase |
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-Non-polymers , 4 types, 637 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-BEZ / | #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: 2.83 Å3/Da / Density % sol: 56.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein Concentration 13.5 mg/mL in 2.5 mM HEPES pH 7.5, precipitant 0.02 M MgCl2, 22% polyacrylic acid 5100 in 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2008 / Details: KOHZU: Double Crystal Si(111) |
Radiation | Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115872 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 98245 / Num. obs: 98245 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.1 / Num. unique all: 9834 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VZ6 Resolution: 1.7→35.9 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 2.223 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 22.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→35.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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