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Yorodumi- PDB-1cs0: Crystal structure of carbamoyl phosphate synthetase complexed at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cs0 | ||||||
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Title | Crystal structure of carbamoyl phosphate synthetase complexed at CYS269 in the small subunit with the tetrahedral mimic l-glutamate gamma-semialdehyde | ||||||
Components | (CARBAMOYL PHOSPHATE SYNTHETASE: ...) x 2 | ||||||
Keywords | LIGASE / TETRAHEDRAL ANALOG / AMIDOTRANSFERASE / SUBSTRATE CHANNELING | ||||||
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 / amino acid biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / protein heterodimerization activity / nucleotide binding / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 | 1cs0.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1cs0.ent.gz | 1002.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cs0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/1cs0 ftp://data.pdbj.org/pub/pdb/validation_reports/cs/1cs0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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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) / Plasmid: PDP412 / Production host: Escherichia coli (E. coli) References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing) #2: Protein | Mass: 41610.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PDP412 / Production host: Escherichia coli (E. coli) References: UniProt: P00907, UniProt: P0A6F1*PLUS, carbamoyl-phosphate synthase (glutamine-hydrolysing) |
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-Non-polymers , 8 types, 4271 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-NET / #10: 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: 3.24 Å3/Da / Density % sol: 61.98 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: batch / pH: 7.4 Details: PEG 8000, TETRAETHYLAMMONIUM CHLORIDE, POTASSIUM CHLORIDE, MANGANESE(II) CHLORIDE, ADENOSINE 5'-DIPHOSPHATE, L-ORNITHINE, L-GLUTAMATE GAMMA-SEMIALDEHYDE, pH 7.4, BATCH, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: OTHER / 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→30 Å / Num. all: 550694 / Num. obs: 550694 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.293 / % possible all: 97.1 |
Reflection | *PLUS Num. measured all: 2729875 |
Reflection shell | *PLUS % possible obs: 97.1 % |
-Processing
Software |
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Refinement | Resolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.011 |