+Open data
-Basic information
Entry | Database: PDB / ID: 4al6 | ||||||
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Title | Crystal structure of the S148ACsy4-crRNA complex | ||||||
Components |
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Keywords | HYDROLASE/RNA / HYDROLASE-RNA COMPLEX / 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 / MOLECULAR REPLACEMENT / Resolution: 2.63 Å | ||||||
Authors | Haurwitz, R.E. / Sternberg, S.H. / Doudna, J.A. | ||||||
Citation | Journal: Embo J. / Year: 2012 Title: Csy4 Relies on an Unusual Catalytic Dyad to Position and Cleave Crispr RNA. Authors: Haurwitz, R.E. / Sternberg, S.H. / 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 | 4al6.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4al6.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 4al6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4al6_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 4al6_full_validation.pdf.gz | 453.9 KB | Display | |
Data in XML | 4al6_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 4al6_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/4al6 ftp://data.pdbj.org/pub/pdb/validation_reports/al/4al6 | HTTPS FTP |
-Related structure data
Related structure data | 4al5SC 4al7C S: Starting model for refinement C: citing same article (ref.) |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21803.910 Da / Num. of mol.: 1 / Mutation: YES 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(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q02MM2 |
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#2: RNA chain | Mass: 5113.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS AERUGINOSA (bacteria) |
#3: Water | ChemComp-HOH / |
Sequence details | THE UNIPROT DATABASE SEQUENCE IS BASED ON AN INCORRECT START CODON. THE DATABASE SEQUENCE IS 20 ...THE UNIPROT DATABASE SEQUENCE IS BASED ON AN INCORRECT START CODON. THE DATABASE SEQUENCE IS 20 AMINO ACIDS SHORTER THAN THE ACTUAL POLYPEPTID |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 45.78 % / Description: NONE |
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Crystal grow | pH: 5 Details: 20% PEG 4000, 150 MM NA CITRATE PH 5.0, 100 MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11588 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→41.73 Å / Num. obs: 8517 / % possible obs: 99.7 % / Observed criterion σ(I): 2.01 / Redundancy: 5.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.44 |
Reflection shell | Resolution: 2.63→2.7 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.54 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AL5 Resolution: 2.63→41.733 Å / SU ML: 0.34 / σ(F): 2.01 / Phase error: 24.61 / Stereochemistry target values: ML Details: RESIDUES -4 TO -3 AND 106 TO 137 IN CHAIN A ARE DISORDERED.
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.218 Å2 / ksol: 0.369 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.63→41.733 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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