+Open data
-Basic information
Entry | Database: PDB / ID: 4qr2 | ||||||
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Title | Crystal structure of Streptococcus pyogenes Cas2 at pH 7.5 | ||||||
Components | CRISPR-associated endoribonuclease Cas2 | ||||||
Keywords | HYDROLASE / FERREDOXIN-LIKE FOLD / deoxyribonuclease | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes serotype M1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bae, E. / Ka, D. / Kim, D. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2014 Title: Structural and functional characterization of Streptococcus pyogenes Cas2 protein under different pH conditions Authors: Ka, D. / Kim, D. / Baek, G. / Bae, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qr2.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qr2.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 4qr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/4qr2 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/4qr2 | HTTPS FTP |
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-Related structure data
Related structure data | 4qr0C 4qr1C 4es2S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 11261.931 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria) Gene: cas2, M5005_Spy1285, SPy_1561 / Production host: Escherichia coli (E. coli) References: UniProt: Q99YS8, Hydrolases; Acting on ester bonds #2: 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: 2 Å3/Da / Density % sol: 38.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% (w/v) PEG 3350, 200mM MgCl2, 100mM HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2014 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.03 Å / Num. obs: 17673 / % possible obs: 99.8 % / Redundancy: 13.7 % / Net I/σ(I): 35.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 14 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 4.63 / Num. unique all: 1723 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ES2 Resolution: 1.8→50.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.895 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.129 / 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: 34.912 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50.03 Å
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Refine LS restraints |
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