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Yorodumi- PDB-1xjw: The Structure of E. coli Aspartate Transcarbamoylase Q137A Mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xjw | ||||||
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Title | The Structure of E. coli Aspartate Transcarbamoylase Q137A Mutant in The R-State | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE REGULATOR / Allosteric enzyme / polar contacts / electrostatics / small angle x-ray scattering / domain closure / intersubunit interactions / TRANSFERASE-TRANSFERASE 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 / Refinement from pre-existing model / Resolution: 2.71 Å | ||||||
Authors | Stieglitz, K.A. / Alam, N. / Xia, J. / Gourinath, S. / Tsuruta, H. / Kantrowitz, E.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: A Single Amino Acid Substitution in the Active Site of Escherichia coli Aspartate Transcarbamoylase Prevents the Allosteric Transition. Authors: Stieglitz, K.A. / Pastra-Landis, S.C. / Xia, J. / Tsuruta, H. / 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 | 1xjw.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xjw.ent.gz | 152 KB | Display | PDB format |
PDBx/mmJSON format | 1xjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xjw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1xjw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1xjw_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 1xjw_validation.cif.gz | 52.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/1xjw ftp://data.pdbj.org/pub/pdb/validation_reports/xj/1xjw | HTTPS FTP |
-Related structure data
Related structure data | 1d09S 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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-Components
#1: Protein | Mass: 34280.059 Da / Num. of mol.: 2 / Mutation: Q137A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrB / Plasmid: pEK 89 / 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 / Plasmid: pEK 89 / 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: 2.5 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 295 K / Method: microdialysis / pH: 5.9 Details: 12 mg/ml Buffer 50 mM Maleic Acid, 3 mM Sodium Azide 1 mM N-Phosphonacetyl-L-Aspartate, pH 5.9, MICRODIALYSIS, temperature 295K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: UCSD MARK III / Detector: AREA DETECTOR / Date: Dec 30, 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: 2.7→7 Å / Num. all: 40234 / Num. obs: 35809 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.0875 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.59 / Num. unique all: 1380 / % possible all: 85 |
-Processing
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Refinement | Method to determine structure: Refinement from pre-existing model Starting model: 1D09 Resolution: 2.71→7 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.71→7 Å
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