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Yorodumi- PDB-2be9: Crystal structure of the CTP-liganded (T-State) aspartate transca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2be9 | ||||||
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Title | Crystal structure of the CTP-liganded (T-State) aspartate transcarbamoylase from the extremely thermophilic archaeon Sulfolobus acidocaldarius | ||||||
Components |
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Keywords | TRANSFERASE / ATCASE / HYPERTHERMOPHILIC / TEMPERATURE / ALLOSTERIC / HOLOENZYME / CTP COMPLEX | ||||||
Function / homology | Function and homology information aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | De Vos, D. / Savvides, S.N. / Van Beeumen, J.J. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2008 Title: Crystal structure of Sulfolobus acidocaldarius aspartate carbamoyltransferase in complex with its allosteric activator CTP. Authors: De Vos, D. / Xu, Y. / Aerts, T. / Van Petegem, F. / Van Beeumen, J.J. #1: Journal: J.Mol.Biol. / Year: 2004 Title: Crystal Structure of T State Aspartate Carbamoyltransferase of the Hyperthermophilic Archaeon Sulfolobus Acidocaldarius. Authors: De Vos, D. / Van Petegem, F. / Remaut, H. / Legrain, C. / Glandorff, N. / Van Beeumen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2be9.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2be9.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 2be9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2be9_validation.pdf.gz | 806.8 KB | Display | wwPDB validaton report |
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Full document | 2be9_full_validation.pdf.gz | 813.2 KB | Display | |
Data in XML | 2be9_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 2be9_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2be9 ftp://data.pdbj.org/pub/pdb/validation_reports/be/2be9 | HTTPS FTP |
-Related structure data
Related structure data | 1pg5S 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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Details | The biological assembly is a dodecamer generated from the heterodimer in the asymmetric unit by the operations: (-y,x-y,z);(-x+y,-x,z);(-y,-x,-z+1/2);(-x+y,y,-z+1/2);(x,x-y,-z+1/2) |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 34332.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Gene: pyrB / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): C600(delta(pyrBI) / References: UniProt: Q55338, aspartate carbamoyltransferase |
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#2: Protein | Mass: 18845.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Gene: pyrI / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): C600(delta(pyrBI) / References: UniProt: P74766 |
-Non-polymers , 4 types, 80 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-CTP / |
#6: 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: 3.29 Å3/Da / Density % sol: 62.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: AMMONIUM SULFATE, SODIUM ACETATE CTP soak, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8034 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 2, 2005 |
Radiation | Monochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8034 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 24875 / Num. obs: 24875 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.56 Å / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1PG5 Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 20.13 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.349 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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