+Open data
-Basic information
Entry | Database: PDB / ID: 2xli | ||||||
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Title | Crystal structure of the Csy4-crRNA complex, monoclinic form | ||||||
Components |
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Keywords | HYDROLASE/RNA / HYDROLASE-RNA COMPLEX / ENDORIBONUCLEASE / CRISPR | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.33 Å | ||||||
Authors | Haurwitz, R.E. / Jinek, M. / Wiedenheft, B. / Zhou, K. / Doudna, J.A. | ||||||
Citation | Journal: Science / Year: 2010 Title: Sequence- and Structure-Specific RNA Processing by a Crispr Endonuclease. Authors: Haurwitz, R.E. / Jinek, M. / Wiedenheft, B. / Zhou, K. / Doudna, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xli.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xli.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/2xli ftp://data.pdbj.org/pub/pdb/validation_reports/xl/2xli | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21849.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: UCBPP-PA14 / Plasmid: PHMGWA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2 (DE3) / References: UniProt: A3KUJ4, UniProt: Q02MM2*PLUS |
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#2: RNA chain | Mass: 5097.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 2-DEOXY MODIFICATION AT G20 / Source: (synth.) PSEUDOMONAS AERUGINOSA (bacteria) |
#3: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE GSFT AT THE N-TERMINUS IS DERIVED FROM THE EXPRESSION VECTOR. THE DOWNSTREAM SEQUENCE ...THE SEQUENCE GSFT AT THE N-TERMINUS IS DERIVED FROM THE EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 5 Details: 200 MM SODIUM CITRATE PH 5.0, 100 MM MAGNESIUM CHLORIDE, 20% (W/V) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11159 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 23, 2009 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11159 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→19.68 Å / Num. obs: 9974 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 37.73 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.33→2.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.35 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.33→19.681 Å / SU ML: 0.37 / σ(F): 1.99 / Phase error: 24.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.423 Å2 / ksol: 0.406 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→19.681 Å
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Refine LS restraints |
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LS refinement shell |
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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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