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Yorodumi- PDB-1t36: Crystal structure of E. coli carbamoyl phosphate synthetase small... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t36 | ||||||
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Title | Crystal structure of E. coli carbamoyl phosphate synthetase small subunit mutant C248D complexed with uridine 5'-monophosphate | ||||||
Components | (Carbamoyl-phosphate synthase ...) x 2 | ||||||
Keywords | LIGASE / channeling / pyrimidine biosynthesis / arginine biosynthesis | ||||||
Function / homology | Function and homology information carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / arginine biosynthetic process / nitrogen compound metabolic process / amino acid binding / glutamine metabolic process ...carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / arginine biosynthetic process / nitrogen compound metabolic process / 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 / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Thoden, J.B. / Huang, X. / Raushel, F.M. / Holden, H.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Long-range allosteric transitions in carbamoyl phosphate synthetase. Authors: Thoden, J.B. / Huang, X. / Kim, 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 | 1t36.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1t36.ent.gz | 977.4 KB | Display | PDB format |
PDBx/mmJSON format | 1t36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/1t36 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/1t36 | HTTPS FTP |
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-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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1 |
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Unit cell |
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Details | Hetero-octamer comprising chains A,B,C,D,E,F,G,H. THese chains, as deposited, represent the biological assebmly |
-Components
-Carbamoyl-phosphate synthase ... , 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) / Gene: CARB, PYRA, B0033 / Plasmid: pet15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing) #2: Protein | Mass: 41493.824 Da / Num. of mol.: 4 / Mutation: C248D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CARA, PYRA, B0032, Z0037, ECS0035 / Plasmid: pet15 / Production host: Escherichia coli (E. coli) References: UniProt: P00907, UniProt: P0A6F1*PLUS, carbamoyl-phosphate synthase (glutamine-hydrolysing) |
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-Non-polymers , 9 types, 3993 molecules
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-ADP / #8: Chemical | ChemComp-ORN / #9: Chemical | ChemComp-NET / #10: Chemical | ChemComp-U / #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 | Temperature: 277 K / Method: batch / pH: 7.4 Details: PEG 8000, tetramethylammonium chloride, potassium chloride, manganese chloride, ornithine, ADP, HEPES, pH 7.4, batch, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.65 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 11, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 433843 / Num. obs: 433843 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.048 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 39976 / Rsym value: 0.203 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1JDB Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 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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