[English] 日本語
Yorodumi- PDB-1vz6: Ornithine Acetyltransferase (ORF6 Gene Product - Clavulanic Acid ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vz6 | ||||||
---|---|---|---|---|---|---|---|
Title | Ornithine Acetyltransferase (ORF6 Gene Product - Clavulanic Acid Biosynthesis) from Streptomyces clavuligerus | ||||||
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 / methione N-acyltransferase activity / amino-acid N-acetyltransferase / clavulanic acid biosynthetic process / acetyl-CoA:L-glutamate N-acetyltransferase activity / arginine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1vz6.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1vz6.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vz6_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1vz6_full_validation.pdf.gz | 460.7 KB | Display | |
Data in XML | 1vz6_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 1vz6_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/1vz6 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/1vz6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, -0.00308, -0.00028), Vector: |
-Components
#1: Protein | Mass: 41653.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source 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 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 60 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→32.11 Å / Num. obs: 29114 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→32.08 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1769009.77 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / ksol: 0.37743 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→32.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|