+Open data
-Basic information
Entry | Database: PDB / ID: 1jdb | ||||||
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Title | CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIA COLI | ||||||
Components | (CARBAMOYL PHOSPHATE ...) x 2 | ||||||
Keywords | LIGASE / AMIDOTRANSFERASE / SYNTHASE | ||||||
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: 2.1 Å | ||||||
Authors | Thoden, J.B. / Holden, H.M. / Wesenberg, G. / Raushel, F.M. / Rayment, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution. Authors: Thoden, J.B. / Raushel, F.M. / Benning, M.M. / Rayment, I. / Holden, H.M. #1: Journal: Biochemistry / Year: 1997 Title: Structure of Carbamoyl Phosphate Synthetase: A Journey of 96 a from Substrate to Product Authors: Thoden, J.B. / Holden, H.M. / Wesenberg, G. / Raushel, F.M. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jdb.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1jdb.ent.gz | 1002.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jdb_validation.pdf.gz | 923 KB | Display | wwPDB validaton report |
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Full document | 1jdb_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1jdb_validation.xml.gz | 141.8 KB | Display | |
Data in CIF | 1jdb_validation.cif.gz | 234.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jdb ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jdb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-CARBAMOYL PHOSPHATE ... , 2 types, 8 molecules BEHKCFIL
#1: Protein | Mass: 117981.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) 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 natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: P00907, UniProt: P0A6F1*PLUS, carbamoyl-phosphate synthase (glutamine-hydrolysing) |
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-Non-polymers , 9 types, 4964 molecules
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-GLN / #8: Chemical | ChemComp-ADP / #9: Chemical | ChemComp-ORN / #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 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: 0.65M TETRAETHYL AMMONIUM CHLORIDE (E4NCL) 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 25MM HEPES PH 7.4. THE CRYSTAL WAS SOAKED INTO: 1.4M E4NCL 8% PEG 8000 250MM KCL 2.5MM ...Details: 0.65M TETRAETHYL AMMONIUM CHLORIDE (E4NCL) 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 25MM HEPES PH 7.4. THE CRYSTAL WAS SOAKED INTO: 1.4M E4NCL 8% PEG 8000 250MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 25MM GLUTAMINE 25MM HEPES PH 7.4 7.5% ETHYLENE GLYCOL. | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 8 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997 |
Radiation | 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: 404724 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.203 / % possible all: 73 |
Reflection shell | *PLUS % possible obs: 73 % / Num. unique obs: 32559 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JDB Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: TNT / Bsol: 556 Å2 / ksol: 1.027 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 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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