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- PDB-2be7: Crystal structure of the unliganded (T-state) aspartate transcarb... -
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Open data
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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 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | De Vos, D. / Savvides, S.N. / Van Beeumen, J. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253.3 KB | Display | ![]() |
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PDB format | ![]() | 202.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6at1S S: Starting model for refinement |
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Similar structure data |
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Links
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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. |
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Components
#1: Protein | Mass: 36266.766 Da / Num. of mol.: 3 / Mutation: V2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P96174, UniProt: D0VWV8*PLUS, ![]() #2: Protein | Mass: 16911.418 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ![]() #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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