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Yorodumi- PDB-1ekx: THE ISOLATED, UNREGULATED CATALYTIC TRIMER OF ASPARTATE TRANSCARB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ekx | ||||||
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Title | THE ISOLATED, UNREGULATED CATALYTIC TRIMER OF ASPARTATE TRANSCARBAMOYLASE COMPLEXED WITH BISUBSTRATE ANALOG PALA (N-(PHOSPHONACETYL)-L-ASPARTATE) | ||||||
Components | ASPARTATE TRANSCARBAMOYLASE | ||||||
Keywords | TRANSFERASE / ATCase catalytic subunit / bisubstrate analog complex | ||||||
Function / homology | Function and homology information aspartate carbamoyltransferase complex / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å | ||||||
Authors | Endrizzi, J.A. / Beernink, P.T. / Alber, T. / Schachman, H.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Binding of bisubstrate analog promotes large structural changes in the unregulated catalytic trimer of aspartate transcarbamoylase: implications for allosteric regulation induced cell migration. Authors: Endrizzi, J.A. / Beernink, P.T. / Alber, T. / Schachman, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ekx.cif.gz | 207 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ekx.ent.gz | 164.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ekx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ekx_validation.pdf.gz | 509.7 KB | Display | wwPDB validaton report |
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Full document | 1ekx_full_validation.pdf.gz | 524.2 KB | Display | |
Data in XML | 1ekx_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 1ekx_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ekx ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ekx | HTTPS FTP |
-Related structure data
Related structure data | |
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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 | The biological assembly is a hetrododecamer constructed of 2 ABC trimers + 3 regulatory dimers (the regulatory chains are not in this structure) |
-Components
#1: Protein | Mass: 34468.301 Da / Num. of mol.: 3 / Fragment: CATALYTIC SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) Keywords: THE BIOLOGICAL ASSEMBLY IS A DODECAMER CONSTRUCTED OF 2 ABC TRIMERS AND 3 REGULATORY DIMERS (THE REGULATORY CHAINS ARE NOT IN THIS STRUCTURE) References: UniProt: P0A786, aspartate carbamoyltransferase #2: Chemical | #3: Chemical | #4: 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: 2.91 Å3/Da / Density % sol: 57.78 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Calcium Acetate, PEG 8000, tris-HCL, 2-mercaptoethanol, PALA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 |
Detector | Type: ADSC / Detector: CCD / Date: Apr 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 125472 / Num. obs: 86079 / % possible obs: 92.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.95→2.03 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.35 / % possible all: 81.1 |
Reflection | *PLUS Num. measured all: 125472 |
Reflection shell | *PLUS % possible obs: 81.1 % / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Resolution: 1.95→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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