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Yorodumi- PDB-1tu0: Aspartate Transcarbamoylase Catalytic Chain Mutant E50A Complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tu0 | ||||||
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Title | Aspartate Transcarbamoylase Catalytic Chain Mutant E50A Complex with Phosphonoacetamide | ||||||
Components |
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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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 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 | 1tu0.cif.gz | 198.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tu0.ent.gz | 158.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tu0_validation.pdf.gz | 488.5 KB | Display | wwPDB validaton report |
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Full document | 1tu0_full_validation.pdf.gz | 556.3 KB | Display | |
Data in XML | 1tu0_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 1tu0_validation.cif.gz | 64.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/1tu0 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/1tu0 | HTTPS FTP |
-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
#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 #3: Chemical | #4: Chemical | #5: 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: The Glu50Ala mutant was crystallized in 100 mM sodium citrate, 1 mM 2-mercaptoethanol, and 15% PEG 8000 pH 7.0. Before mounting, 50 mM PAM was added and the crystal soaked, pH 6.0, ...Details: The Glu50Ala mutant was crystallized in 100 mM sodium citrate, 1 mM 2-mercaptoethanol, and 15% PEG 8000 pH 7.0. Before mounting, 50 mM PAM was added and the crystal soaked, pH 6.0, 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: Mar 31, 1998 |
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: 2.55→30 Å / Num. obs: 37788 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.37 |
Reflection shell | Resolution: 2.55→2.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.32 / % possible all: 89.53 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED Resolution: 2.55→30 Å / Num. parameters: 30387 / Num. restraintsaints: 29984 / Cross valid method: THROUGHOUT / 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: 7585.11 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→30 Å
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Refine LS restraints |
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