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Yorodumi- PDB-2be7: Crystal structure of the unliganded (T-state) aspartate transcarb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2be7 | ||||||
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Title | Crystal structure of the unliganded (T-state) aspartate transcarbamoylase of the psychrophilic bacterium Moritella profunda | ||||||
Components |
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Keywords | TRANSFERASE / ATCASE / PSYCHROPHILIC / COLD ADAPTATION / ALLOSTERIC / HOLOENZYME | ||||||
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 Similarity search - Function | ||||||
Biological species | Moritella profunda (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | De Vos, D. / Savvides, S.N. / Van Beeumen, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural investigation of cold activity and regulation of aspartate carbamoyltransferase from the extreme psychrophilic bacterium Moritella profunda. Authors: De Vos, D. / Xu, Y. / Hulpiau, P. / Vergauwen, B. / Van Beeumen, J.J. #1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2005 Title: Expression, purification, crystallization and preliminary X-ray crystallographic studies of a cold-adapted aspartate carbamoyltransferase from Moritella profunda. Authors: De Vos, D. / Hulpiau, P. / Vergauwen, B. / Savvides, S.N. / Van Beeumen, J. | ||||||
History |
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Remark 999 | Sequence No suitable database references were found at time of processing |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2be7.cif.gz | 253.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2be7.ent.gz | 202.5 KB | Display | PDB format |
PDBx/mmJSON format | 2be7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2be7_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
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Full document | 2be7_full_validation.pdf.gz | 469.6 KB | Display | |
Data in XML | 2be7_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 2be7_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2be7 ftp://data.pdbj.org/pub/pdb/validation_reports/be/2be7 | HTTPS FTP |
-Related structure data
Related structure data | 6at1S 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 second part of the dodecameric biological assembly is generated by the operation: -x,-x+y,-z-1/3. |
-Components
#1: Protein | Mass: 36266.766 Da / Num. of mol.: 3 / Mutation: V2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moritella profunda (bacteria) / Gene: pyrB / Plasmid: pACYC-Duet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P96174, UniProt: D0VWV8*PLUS, aspartate carbamoyltransferase #2: Protein | Mass: 16911.418 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moritella profunda (bacteria) / Gene: pyrI / Plasmid: pACYC-Duet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P96175, UniProt: D0VWV9*PLUS #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: 3.13 Å3/Da / Density % sol: 60.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10 mg/ml, 0.1 M Tris, 1.5 M ammonium sulfate , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.92 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 10, 2004 |
Radiation | Monochromator: double crystal focussing monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. all: 45685 / Num. obs: 45685 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.85→2.93 Å / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 6AT1 Resolution: 2.85→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU B: 27.764 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.082 / ESU R Free: 0.363 / 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: 51.473 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.922 Å / Total num. of bins used: 20
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