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Yorodumi- PDB-4amu: Structure of ornithine carbamoyltransferase from Mycoplasma penet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4amu | ||||||
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Title | Structure of ornithine carbamoyltransferase from Mycoplasma penetrans with a P321 space group | ||||||
Components | ORNITHINE CARBAMOYLTRANSFERASE, CATABOLICOrnithine transcarbamylase | ||||||
Keywords | TRANSFERASE / ORNITHINE TRANSCARBAMOYLASE / HYDROLASE | ||||||
Function / homology | Function and homology information arginine deiminase pathway / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine catabolic process to ornithine / amino acid binding / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOPLASMA PENETRANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Gallego, P. / Benach, J. / Planell, R. / Querol, E. / Perez-Pons, J.A. / Reverter, D. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structural Characterization of the Enzymes Composing the Arginine Deiminase Pathway in Mycoplasma Penetrans. Authors: Gallego, P. / Planell, R. / Benach, J. / Querol, E. / Perez-Pons, J.A. / Reverter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4amu.cif.gz | 278.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4amu.ent.gz | 226.8 KB | Display | PDB format |
PDBx/mmJSON format | 4amu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4amu ftp://data.pdbj.org/pub/pdb/validation_reports/am/4amu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 40864.414 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOPLASMA PENETRANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EVF5, ornithine carbamoyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.79 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.42 Å / Num. obs: 77424 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.425 Å / SU ML: 0.32 / σ(F): 0.02 / Phase error: 20.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.822 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→49.425 Å
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Refine LS restraints |
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LS refinement shell |
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