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Yorodumi- PDB-1c3o: CRYSTAL STRUCTURE OF THE CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c3o | ||||||
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Title | CRYSTAL STRUCTURE OF THE CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT MUTANT C269S WITH BOUND GLUTAMINE | ||||||
Components | (CARBAMOYL PHOSPHATE SYNTHETASE: ...) x 2 | ||||||
Keywords | LIGASE / AMIDOTRANSFERASE / MICHAELIS COMPLEX / ATP-GRASP | ||||||
Function / homology | Function and homology information carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / : / pyrimidine nucleobase biosynthetic process / arginine biosynthetic process / glutaminase activity / amino acid binding ...carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / : / pyrimidine nucleobase biosynthetic process / arginine biosynthetic process / glutaminase activity / amino acid binding / glutamine metabolic process / 'de novo' UMP biosynthetic process / amino acid biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / protein heterodimerization activity / nucleotide binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Thoden, J.B. / Huang, X. / Raushel, F.M. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway. Authors: Thoden, J.B. / Huang, X. / Raushel, F.M. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c3o.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1c3o.ent.gz | 972.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c3o_validation.pdf.gz | 919.8 KB | Display | wwPDB validaton report |
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Full document | 1c3o_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1c3o_validation.xml.gz | 138.2 KB | Display | |
Data in CIF | 1c3o_validation.cif.gz | 224.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3o ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3o | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-CARBAMOYL PHOSPHATE SYNTHETASE: ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 117981.750 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Bacteria (eubacteria) References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing) #2: Protein | Mass: 41465.816 Da / Num. of mol.: 4 / Mutation: C269S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Bacteria (eubacteria) References: UniProt: P00907, UniProt: P0A6F1*PLUS, carbamoyl-phosphate synthase (glutamine-hydrolysing) |
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-Non-polymers , 9 types, 3755 molecules
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-PO4 / #7: Chemical | ChemComp-ADP / #8: Chemical | ChemComp-ORN / #9: Chemical | ChemComp-GLN / #10: Chemical | ChemComp-NET / #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.35 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: batch / pH: 7.4 Details: PEG-8000, MANGANESE CHLORIDE, TETRAETHYLAMMONIUM CHLORIDE, POTASSIUM CHLORIDE, BERYLLIUM FLUORIDE, ADENOSINE 5'-DIPHOSPHATE,L-ORNITHINE, L-GLUTAMINE, HEPPS, pH 7.4, BATCH, temperature 278K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.7005 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Feb 24, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7005 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 476527 / Num. obs: 476527 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.282 / % possible all: 97.9 |
Reflection | *PLUS Num. measured all: 2532077 |
Reflection shell | *PLUS % possible obs: 97.9 % / Num. unique obs: 47060 / Num. measured obs: 201948 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Resolution: 2.1→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor all: 0.189 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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