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Yorodumi- PDB-1vz8: Ornithine Acetyltransferase (ORF6 Gene Product - Clavulanic Acid ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vz8 | ||||||
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Title | Ornithine Acetyltransferase (ORF6 Gene Product - Clavulanic Acid Biosynthesis) from Streptomyces clavuligerus (SeMet structure) | ||||||
Components | ORNITHINE ACETYL-TRANSFERASE | ||||||
Keywords | TRANSFERASE / ORNITHINE ACETYLTRANSFERASE / CLAVULANIC ACID / N-ACETYL- ORNITHINE / N-ACETYL-GLUTAMATE / ANTIBIOTIC | ||||||
Function / homology | Function and homology information glutamate N-acetyltransferase / glutamate N-acetyltransferase activity / ornithine biosynthetic process / L-methionine N-acyltransferase activity / amino-acid N-acetyltransferase / clavulanic acid biosynthetic process / L-glutamate N-acetyltransferase activity / arginine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å | ||||||
Authors | Elkins, J.M. / Kershaw, N.J. / Schofield, C.J. | ||||||
Citation | Journal: Biochem.J. / Year: 2005 Title: X-Ray Crystal Structure of Ornithine Acetyltransferase from the Clavulanic Acid Biosynthesis Gene Cluster. Authors: Elkins, J.M. / Kershaw, N.J. / Schofield, C.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vz8.cif.gz | 269.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vz8.ent.gz | 227.6 KB | Display | PDB format |
PDBx/mmJSON format | 1vz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/1vz8 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/1vz8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 42028.770 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SELENOMETHIONINE-SUBSTITUTED / Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | THERE IS A BREAK IN THE CHAIN BETWEEN RESIDUES 180 AND 181, DUE TO THE AUTO-PROTEOLYTIC SELF- ...THERE IS A BREAK IN THE CHAIN BETWEEN RESIDUES 180 AND 181, DUE TO THE AUTO-PROTEOLYTI | |
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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: 2.3 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | pH: 8 Details: PROTEIN AT 12MG/ML MIXED 1:1 WITH A SOLUTION OF: 1.2M (NH4)2SO4, 40MM NH4H2PO4, 0.1M TRIS PH 8.0, 6% GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.89 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→20.5 Å / Num. obs: 40839 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.75→23.67 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1847476.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / ksol: 0.380215 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→23.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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