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Yorodumi- PDB-1oth: CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMOYLASE COMPLEXED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oth | |||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-PHOSPHONACETYL-L-ORNITHINE | |||||||||
Components | PROTEIN (ORNITHINE TRANSCARBAMOYLASE) | |||||||||
Keywords | TRANSFERASE / TRANSCARBAMOYLASE | |||||||||
Function / homology | Function and homology information response to biotin / ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / Urea cycle / citrulline biosynthetic process / arginine biosynthetic process via ornithine / Mitochondrial protein import ...response to biotin / ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / Urea cycle / citrulline biosynthetic process / arginine biosynthetic process via ornithine / Mitochondrial protein import / urea cycle / midgut development / amino acid binding / response to zinc ion / phosphate ion binding / liver development / response to insulin / phospholipid binding / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / mitochondrion / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Shi, D. / Morizono, H. / Ha, Y. / Aoyagi, M. / Tuchman, N. / Allewell, N.M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: 1.85-A resolution crystal structure of human ornithine transcarbamoylase complexed with N-phosphonacetyl-L-ornithine. Catalytic mechanism and correlation with inherited deficiency. Authors: Shi, D. / Morizono, H. / Ha, Y. / Aoyagi, M. / Tuchman, M. / Allewell, N.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oth.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oth.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 1oth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/1oth ftp://data.pdbj.org/pub/pdb/validation_reports/ot/1oth | HTTPS FTP |
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-Related structure data
Related structure data | 2ortS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36106.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-PHOSPHONACETYL-L-ORNITHINE BIND ACTIVE SITE / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PETOTCII / Production host: Escherichia coli (E. coli) / References: UniProt: P00480 |
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#2: Chemical | ChemComp-PAO / |
#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: 4.8 Å3/Da / Density % sol: 73 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 20 MM TRISAC, 2MM EDTA, 20MM KCL, 4MM PALO PH=7.4, pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 |
Detector | Date: Mar 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. obs: 51424 / % possible obs: 86.4 % / Observed criterion σ(I): 1 / Redundancy: 28 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.85→1.93 Å / Redundancy: 25 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.4 / % possible all: 63.3 |
Reflection | *PLUS Num. measured all: 1393080 |
Reflection shell | *PLUS % possible obs: 63.3 % / Num. unique obs: 51424 / Rmerge(I) obs: 0.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ORT Resolution: 1.85→40 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 17.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.251 / % reflection Rfree: 8.6 % / Rfactor Rwork: 0.243 / Rfactor obs: 0.243 |