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Yorodumi- PDB-1dxh: Catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dxh | ||||||
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Title | Catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa | ||||||
Components | ORNITHINE CARBAMOYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / TRANSCARBAMYLASE | ||||||
Function / homology | Function and homology information arginine deiminase pathway / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / arginine catabolic process to ornithine / amino acid binding / cytoplasm Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sainz, G. / Vicat, J. / Kahn, R. / Duee, E. / Tricot, C. / Stalon, V. / Dideberg, O. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Allosteric Active Form of Catabolic Ornithine Carbamoyltransferase from Pseudomonas Aeruginosa Authors: Sainz, G. / Vicat, J. / Kahn, R. / Duee, E. / Tricot, C. / Stalon, V. / Dideberg, O. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Purification, Crystallization and Preliminary X-Ray Analysis of Catabolic Ornithine Carbamoyltransferase from Pseudomonas Aeruginosa Authors: Sainz, G. / Vicat, J. / Kahn, R. / Tricot, C. / Stalon, V. / Dideberg, O. #2: Journal: J.Mol.Biol. / Year: 1998 Title: Allosteric Regulation in Pseudomonas Aeruginosa Catabolic Ornithine Carbamoyltransferase Revisited : Association of Concerted Homotropic Cooperative Interactions and Local Heterotropic Effects Authors: Tricot, C. / Villeret, V. / Sainz, G. / Dideberg, O. / Stalon, V. #3: Journal: Eur.J.Biochem. / Year: 1998 Title: Kinetic Studies of Allosteric Catabolic Ornithine Carbamoyltransferase from Pseudomonas Aeruginosa Authors: Sainz, G. / Tricot, C. / Foray, M.F. / Marion, D. / Dideberg, O. / Stalon, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dxh.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dxh.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dxh_validation.pdf.gz | 377.7 KB | Display | wwPDB validaton report |
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Full document | 1dxh_full_validation.pdf.gz | 383.4 KB | Display | |
Data in XML | 1dxh_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 1dxh_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dxh ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dxh | HTTPS FTP |
-Related structure data
Related structure data | 1ortS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | BIOLOGICAL_UNIT: DODECAMERTHE ASYMMETRIC UNIT CONTAINS 3 SULPHATE IONS.THE FIRST, SO4 340, IS ORDERED, WHILE THE OTHERS AREDISORDERED AND LIE ON THE THREE-FOLD AXIS RELATING(X,Y,Z) ,(1-Z , X, 1-Y) AND (Y, 1-Z, 1-X) AND AREREPRESENTED BY THE SO4 RESIDUES 338 AND 339. THREE WATER MOLECULES ARE ALSO ON THE THREE-FOLD AXIS,601,603 AND 624. THE LAST ONE IS ASSOCIATED WITH THESO4 RESIDUE 339 |
-Components
#1: Protein | Mass: 38030.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: P08308, ornithine carbamoyltransferase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.67 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.20 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 47.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: BRUKER NONIUS / Detector: AREA DETECTOR |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 13231 / % possible obs: 95.4 % / Redundancy: 5.58 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.075 |
Reflection shell | Resolution: 2.5→2.61 Å / Rsym value: 0.252 / % possible all: 67.3 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. measured all: 80597 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 65.5 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ORT Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 32.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPH19X.PRO |