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Yorodumi- PDB-2hse: Structure of D236A E. coli Aspartate Transcarbamoylase in the pre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hse | ||||||
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Title | Structure of D236A E. coli Aspartate Transcarbamoylase in the presence of phosphonoacetamide and l-Aspartate at 2.60 A resolution | ||||||
Components | (Aspartate carbamoyltransferase ...) x 2 | ||||||
Keywords | TRANSFERASE / domain closure / allosteric transition | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Wang, J. / Kantrowitz, E.R. | ||||||
Citation | Journal: To be Published Title: The allosteric transition induced by the aspartate binding to Aspartate Transcarbamoylase Authors: Wang, J. / Eldo, J. / 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 | 2hse.cif.gz | 195.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hse.ent.gz | 155.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hse_validation.pdf.gz | 507 KB | Display | wwPDB validaton report |
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Full document | 2hse_full_validation.pdf.gz | 558.4 KB | Display | |
Data in XML | 2hse_validation.xml.gz | 45 KB | Display | |
Data in CIF | 2hse_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/2hse ftp://data.pdbj.org/pub/pdb/validation_reports/hs/2hse | HTTPS FTP |
-Related structure data
Related structure data | 2a0fS 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
-Aspartate carbamoyltransferase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 34293.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrB / Plasmid: pEK54 / 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: pEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3 |
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-Non-polymers , 5 types, 357 molecules
#3: Chemical | ChemComp-PO4 / | ||||||
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#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.46 % |
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Crystal grow | Temperature: 293 K / Method: microdialysis / pH: 5.8 Details: 50mM maleic acid, 3mM sodium azide, 10mM phosphonoacetamide, 20mM L-aspartate, pH 5.8, MICRODIALYSIS, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 40149 / Num. obs: 40109 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.579 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2A0F Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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