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Open data
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Basic information
Entry | Database: PDB / ID: 3wvo | ||||||
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Title | Crystal structure of Thermobifida fusca Cse1 | ||||||
![]() | CRISPR-associated protein, Cse1 family | ||||||
![]() | CELL INVASION / CRISPR / Cascade / CasA | ||||||
Function / homology | Topoisomerase I; Chain A, domain 4 - #100 / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / Topoisomerase I; Chain A, domain 4 / Orthogonal Bundle / Mainly Alpha / CRISPR-associated protein, Cse1 family![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yuan, Y.A. / Tay, M. | ||||||
![]() | ![]() Title: Crystal structure of Thermobifida fusca Cse1 reveals target DNA binding site. Authors: Tay, M. / Liu, S. / Yuan, Y.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 641.7 KB | Display | ![]() |
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PDB format | ![]() | 539.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4h3tS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 61828.496 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG8000, Cacodylate, potassium chloride, magnesium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 39600 / Num. obs: 35245 / % possible obs: 89.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 3.3→3.36 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4H3T Resolution: 3.31→48.37 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 40.337 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 73.488 Å2
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Refinement step | Cycle: LAST / Resolution: 3.31→48.37 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.31→3.396 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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