+Open data
-Basic information
Entry | Database: PDB / ID: 4zkj | ||||||||||||
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Title | Crystal structure of CRISPR-associated protein | ||||||||||||
Components | CRISPR-associated protein Cas1 | ||||||||||||
Keywords | UNKNOWN FUNCTION / CRISPR / Cas | ||||||||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Streptococcus pyogenes M1 476 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | ||||||||||||
Authors | Ka, D. / Bae, E. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: Structure / Year: 2016 Title: Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System Authors: Ka, D. / Lee, H. / Jung, Y.D. / Kim, K. / Seok, C. / Suh, N. / Bae, E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zkj.cif.gz | 250 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zkj.ent.gz | 212.9 KB | Display | PDB format |
PDBx/mmJSON format | 4zkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/4zkj ftp://data.pdbj.org/pub/pdb/validation_reports/zk/4zkj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 34087.445 Da / Num. of mol.: 2 / Fragment: UNP residues 2-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes M1 476 (bacteria) Gene: cas1, M1GAS476_0831 / Production host: Escherichia coli (E. coli) References: UniProt: J7M1H5, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.6/0.6M Na/KH2PO4, 27% (w/v) glycerol and 130 mM HEPES pH 7.0 |
-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: Dec 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 579853 / Num. obs: 579520 / % possible obs: 99.6 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.25 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 3.97 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→35.14 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 10.429 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.152 / 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: 70.034 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→35.14 Å
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Refine LS restraints |
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