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Yorodumi- PDB-4mak: Crystal structure of a putative ssRNA endonuclease Cas2, CRISPR a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mak | ||||||
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Title | Crystal structure of a putative ssRNA endonuclease Cas2, CRISPR adaptation protein from E.coli | ||||||
Components | CRISPR-associated endoribonuclease Cas2 | ||||||
Keywords | HYDROLASE / CAS2 / CRISPR / MCSG / PSI-BIOLOGY / Structural Genomics / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information CRISPR-cas system / maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Nocek, B. / Skarina, T. / Brown, G. / Yakunin, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of a putative ssRNA endonuclease Cas2, CRISPR adaptation protein from E.coli Authors: Nocek, B. / Skarina, T. / Brown, G. / Yakunin, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mak.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mak.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 4mak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/4mak ftp://data.pdbj.org/pub/pdb/validation_reports/ma/4mak | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10527.212 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 substr. MG1655 / Gene: ygbF, cas2, b2754, JW5438 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P45956, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-PEG / | #3: 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: 1.65 Å3/Da / Density % sol: 25.36 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG3350, 0.1M KCl, 10mM MgCl2, Na Citr 0.1M ph 6, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2011 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→33.03 Å / Num. all: 57350 / Num. obs: 53336 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.1→1.12 Å / Rmerge(I) obs: 0.43 / % possible all: 52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→33.03 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.863 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.034 / ESU R Free: 0.037 / 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: 22.269 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→33.03 Å
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Refine LS restraints |
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