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Yorodumi- PDB-1c9y: HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c9y | ||||||
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Title | HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CATALYTIC MECHANISM | ||||||
Components | ORNITHINE CARBAMOYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ORNITHINE TRANSCARBAMYLASE / SUBSTRATE RECOGNITION / CATALYTIC MECHANISM | ||||||
Function / homology | Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / NORVALINE / : Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Shi, D. / Yu, X. / Morizono, H. / Tuchman, M. / Allewell, N.M. | ||||||
Citation | Journal: Proteins / Year: 2000 Title: Crystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate and L-norvaline at 1.9 A resolution. Authors: Shi, D. / Morizono, H. / 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 | 1c9y.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c9y.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c9y_validation.pdf.gz | 452.3 KB | Display | wwPDB validaton report |
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Full document | 1c9y_full_validation.pdf.gz | 455.4 KB | Display | |
Data in XML | 1c9y_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 1c9y_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c9y ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c9y | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 36106.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00480, ornithine carbamoyltransferase |
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#2: Chemical | ChemComp-NVA / |
#3: Chemical | ChemComp-CP / |
#4: 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: 4.55 Å3/Da / Density % sol: 72.97 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 400, AMMONIUM SULFATE, POTASSIUM CHLORIDE, EDTA, TRIS ACETATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.0702 |
Detector | Detector: IMAGE PLATE / Date: Oct 29, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0702 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35 Å / Num. obs: 52412 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 16 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 54.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.149 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 799411 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.186 / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_dihedral_angle_deg / Dev ideal: 23.96 |