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Yorodumi- PDB-1ce8: CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIS COLI WITH COMPLEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ce8 | ||||||
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Title | CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIS COLI WITH COMPLEXED WITH THE ALLOSTERIC LIGAND IMP | ||||||
Components | (PROTEIN (CARBAMOYL-PHOSPHATE ...) x 2 | ||||||
Keywords | LIGASE IMP / IMP / ALLOSTERIC LIGAND | ||||||
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 / glutamine metabolic process ...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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Thoden, J.B. / Raushel, F.M. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase. Authors: Thoden, J.B. / Raushel, F.M. / Wesenberg, G. / 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 | 1ce8.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1ce8.ent.gz | 981.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ce8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/1ce8 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/1ce8 | HTTPS FTP |
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-Related structure data
Related structure data | 1a9xS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-PROTEIN (CARBAMOYL-PHOSPHATE ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 117982.688 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: LONG CHAIN / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing) #2: Protein | Mass: 41480.895 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SHORT CHAIN / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P0A6F1, carbamoyl-phosphate synthase (glutamine-hydrolysing) |
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-Non-polymers , 9 types, 4117 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-IMP / #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: 3.2 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 445013 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.221 / % possible all: 81 |
Reflection shell | *PLUS % possible obs: 81 % / Num. unique obs: 38417 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A9X Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: MISSING RESIDUES THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST ...Details: MISSING RESIDUES THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP
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Solvent computation | Solvent model: TNT / Bsol: 403.8 Å2 / ksol: 0.881 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
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: 5D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection Rfree: 22250 / Rfactor all: 0.192 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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