+Open data
-Basic information
Entry | Database: PDB / ID: 4h7a | ||||||
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Title | Crystal structure of CasB from Thermus thermophilus | ||||||
Components | CRISPR-associated protein Cse2 | ||||||
Keywords | DNA BINDING PROTEIN / CRISPR / Cascade / CasB / CRISPR-assoicated protein / Nucleic acid binding protein | ||||||
Function / homology | CRISPR-associated protein Cse2 / CRISPR-associated protein Cse2 / Cse2 superfamily / CRISPR-associated protein Cse2 (CRISPR_cse2) / Peroxidase; domain 1 / defense response to virus / Orthogonal Bundle / Mainly Alpha / CRISPR-associated protein Cse2 Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Ke, A. / Nam, K.H. | ||||||
Citation | Journal: Febs Lett. / Year: 2012 Title: Nucleic acid binding surface and dimer interface revealed by CRISPR-associated CasB protein structures. Authors: Nam, K.H. / Huang, Q. / Ke, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h7a.cif.gz | 141.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h7a.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 4h7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/4h7a ftp://data.pdbj.org/pub/pdb/validation_reports/h7/4h7a | HTTPS FTP |
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-Related structure data
Related structure data | 4h79C 2zcaS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 1 - 156 / Label seq-ID: 13 - 168
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Details | Biological Assembly has been characterized by electron microscopy |
-Components
#1: Protein | Mass: 19423.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: cse2, TTHB189 / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: Q53VY0 #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: 2.77 Å3/Da / Density % sol: 55.65 % |
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Crystal grow | Temperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 0.1M MES, pH 5.7-5.9, 50 mM MgSO4, 5% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 31, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 12996 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 86.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZCA Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.427 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
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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 max: 165.38 Å2 / Biso mean: 64.2504 Å2 / Biso min: 22.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 159 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.19 / Type: LOCAL / Weight: 0.05
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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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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