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Yorodumi- PDB-1a9x: CARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a9x | ||||||
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Title | CARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HYDROLYSIS | ||||||
Components | (CARBAMOYL PHOSPHATE SYNTHETASE ...) x 2 | ||||||
Keywords | AMIDOTRANSFERASE / THIOESTER | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Thoden, J. / Holden, H. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis. Authors: Thoden, J.B. / Miran, S.G. / Phillips, J.C. / Howard, A.J. / 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 | 1a9x.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1a9x.ent.gz | 992.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a9x_validation.pdf.gz | 912.7 KB | Display | wwPDB validaton report |
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Full document | 1a9x_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1a9x_validation.xml.gz | 142.1 KB | Display | |
Data in CIF | 1a9x_validation.cif.gz | 232 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/1a9x ftp://data.pdbj.org/pub/pdb/validation_reports/a9/1a9x | HTTPS FTP |
-Related structure data
Related structure data | 1jdbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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: 117956.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00968 #2: Protein | Mass: 41254.520 Da / Num. of mol.: 4 / Mutation: H353N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00907, UniProt: P0A6F1*PLUS |
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-Non-polymers , 8 types, 4631 molecules
#3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-CL / #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: 3.25 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: 0.65M NET4CL 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 THEN SOAKED INTO: 1.4M NET4CL 8% PEG 8000 250MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ...Details: 0.65M NET4CL 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 THEN SOAKED INTO: 1.4M NET4CL 8% PEG 8000 250MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 7.5% ETHYLENE GLYCOL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 8 / Method: batch method / Details: Thoden, J.B., (1995) Acta Crysta., D51, 827. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 17-ID / Wavelength: 1.2 |
Detector | Type: BRUKER / Detector: CCD / Date: Nov 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 700998 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 2 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 4 / Rsym value: 0.275 / % possible all: 91 |
Reflection | *PLUS Num. measured all: 1676492 |
Reflection shell | *PLUS % possible obs: 91 % / Num. unique obs: 85888 / Num. measured obs: 170785 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JDB Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: TNT / Bsol: 290.8 Å2 / ksol: 0.99 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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