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Open data
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Basic information
Entry | Database: PDB / ID: 4qr1 | ||||||
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Title | Crystal structure of Streptococcus pyogenes Cas2 at pH 6.5 | ||||||
![]() | CRISPR-associated endoribonuclease Cas2 | ||||||
![]() | HYDROLASE / FERREDOXIN-LIKE FOLD / deoxyribonuclease | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bae, E. / Ka, D. / Kim, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.4 KB | Display | ![]() |
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PDB format | ![]() | 61.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.1 KB | Display | ![]() |
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Full document | ![]() | 416.1 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qr0C ![]() 4qr2C ![]() 4es2S C: citing same article ( 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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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.) ![]() Gene: cas2, M5005_Spy1285, SPy_1561 / Production host: ![]() ![]() References: UniProt: Q99YS8, Hydrolases; Acting on ester bonds #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% (w/v) PEG 8000, 200mM Na acetate, 100mM Na cacodylate pH 6.5 , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
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: 2.193→50 Å / Num. obs: 9551 / % possible obs: 96.8 % / Redundancy: 12.8 % / Net I/σ(I): 15.55 |
Reflection shell | Resolution: 2.193→2.28 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 6.58 / Num. unique all: 951 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ES2 Resolution: 2.193→49.83 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.958 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.237 / 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: 51.236 Å2
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Refinement step | Cycle: LAST / Resolution: 2.193→49.83 Å
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Refine LS restraints |
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