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Yorodumi- PDB-1tug: Aspartate Transcarbamoylase Catalytic Chain Mutant E50A Complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tug | ||||||
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Title | Aspartate Transcarbamoylase Catalytic Chain Mutant E50A Complex with Phosphonoacetamide, Malonate, and Cytidine-5-Prime-Triphosphate (CTP) | ||||||
Components | (Aspartate carbamoyltransferase ...) x 2 | ||||||
Keywords | HYDROLASE/HYDROLASE REGULATOR / protein structure-function / site specific mutagenesis / domain closure / allosteric transition / HYDROLASE-HYDROLASE REGULATOR COMPLEX | ||||||
Function / homology | Function and homology information aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Stieglitz, K. / Stec, B. / Baker, D.P. / Kantrowitz, E.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Monitoring the Transition from the T to the R State in E.coli Aspartate Transcarbamoylase by X-ray Crystallography: Crystal Structures of the E50A Mutant Enzyme in Four Distinct Allosteric States. Authors: Stieglitz, K. / Stec, B. / Baker, D.P. / Kantrowitz, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tug.cif.gz | 212.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tug.ent.gz | 168.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/1tug ftp://data.pdbj.org/pub/pdb/validation_reports/tu/1tug | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Aspartate carbamoyltransferase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 34279.074 Da / Num. of mol.: 2 / Mutation: E50A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRB, B4245, C5345, Z5856, ECS5222, SF4245, S4507 / Plasmid: pEK91 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase #2: Protein | Mass: 17143.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRI, B4244, C5344, Z5855, ECS5221 / Plasmid: pEK91 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3 |
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-Non-polymers , 5 types, 706 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.23 Å3/Da / Density % sol: 44.9 % |
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Crystal grow | Temperature: 295 K / pH: 6 Details: 100 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA and 1.0 mM CTP pH 6.0 then soaked for 24 hours in 100 mM malonate, 2 mM CTP, 3 mM sodium azide, 2 mM 2-mercaptoethanol, and 15% PEG ...Details: 100 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA and 1.0 mM CTP pH 6.0 then soaked for 24 hours in 100 mM malonate, 2 mM CTP, 3 mM sodium azide, 2 mM 2-mercaptoethanol, and 15% PEG 8000 pH 7.0. Before mounting, 50 mM PAM was added and the crystal allowed to soak until data collected., MICRODIALYSIS, temperature 295K, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: UCSD MARK III / Detector: AREA DETECTOR / Date: Dec 31, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 67173 / % possible obs: 88.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.41 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 1.09 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.09 / % possible all: 68.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED Resolution: 2.1→30 Å / Num. parameters: 32065 / Num. restraintsaints: 30136 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: GEOMETRY OF STRUCTURES WAS CHECKED AND CORRECTED IN CNS. FINAL RUNS FOR THIS ENTRY WERE CHECKED AGAINST SFCHECK YIELDED R-FACTOR AND R-FREE.
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7994.05 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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