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Yorodumi- PDB-1ep9: HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ep9 | ||||||
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Title | HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CONFORMATIONAL CHANGE | ||||||
Components | ORNITHINE TRANSCARBAMYLASE | ||||||
Keywords | TRANSFERASE / protein-substrate complex | ||||||
Function / homology | Function and homology information response to biotin / ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / midgut development / Urea cycle / citrulline biosynthetic process / arginine biosynthetic process via ornithine ...response to biotin / ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / midgut development / Urea cycle / citrulline biosynthetic process / arginine biosynthetic process via ornithine / Mitochondrial protein import / urea cycle / 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 / Resolution: 2.4 Å | ||||||
Authors | Shi, D. / Morizono, H. / Yu, X. / Allewell, N.M. / Tuchman, M. | ||||||
Citation | Journal: Biochem.J. / Year: 2001 Title: Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes. Authors: Shi, D. / Morizono, H. / Yu, X. / Tong, L. / Allewell, N.M. / Tuchman, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ep9.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ep9.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ep9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ep9_validation.pdf.gz | 439.4 KB | Display | wwPDB validaton report |
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Full document | 1ep9_full_validation.pdf.gz | 444.7 KB | Display | |
Data in XML | 1ep9_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 1ep9_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/1ep9 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/1ep9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a trimer constructed from chain A a symmetry partner generated by the three-fold. |
-Components
#1: Protein | Mass: 36106.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET 21A+ / Production host: Escherichia coli (E. coli) / References: UniProt: P00480, ornithine carbamoyltransferase |
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#2: Chemical | ChemComp-CP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.57 Å3/Da / Density % sol: 73.09 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 20 MM TRISAC, 2MM EDTA, 20MM KCL, 4MM PALO, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 73 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 333653 / Num. obs: 26061 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.8 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.4→2.54 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.402 / Num. unique all: 4070 / % possible all: 93.2 |
Reflection | *PLUS Num. measured all: 333653 |
Reflection shell | *PLUS % possible obs: 93.2 % |
-Processing
Software |
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Refinement | Resolution: 2.4→20 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.271 / Rfactor Rwork: 0.219 |