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Yorodumi- PDB-6kqr: A pre-assembled molecular-helical Cascade backbone of Csy3 subuni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kqr | ||||||
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Title | A pre-assembled molecular-helical Cascade backbone of Csy3 subunits from Zymomonas mobilis | ||||||
Components | CRISPR-associated protein Csy3 family | ||||||
Keywords | RNA BINDING PROTEIN / CRISPR / Cascade / Csy3 / helical backbone | ||||||
Function / homology | CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / : / CRISPR-associated protein, Csy3 family Function and homology information | ||||||
Biological species | Zymomonas mobilis subsp. mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.899 Å | ||||||
Authors | Gu, D.H. / Ha, S.C. / Kim, J.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Front Microbiol / Year: 2019 Title: A CRISPR RNA Is Closely Related With the Size of the Cascade Nucleoprotein Complex. Authors: Gu, D.H. / Ha, S.C. / Kim, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kqr.cif.gz | 446.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kqr.ent.gz | 368.9 KB | Display | PDB format |
PDBx/mmJSON format | 6kqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/6kqr ftp://data.pdbj.org/pub/pdb/validation_reports/kq/6kqr | HTTPS FTP |
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-Related structure data
Related structure data | 5uz9S 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: 38280.285 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria) Gene: ZMO2_ZMO0684, ZMO3_ZMO0684 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R4RXD4, UniProt: Q5NPQ2*PLUS |
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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: 3.95 Å3/Da / Density % sol: 68.88 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH 6.5, 2.0M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: Jul 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.899→30 Å / Num. obs: 86087 / % possible obs: 98.4 % / Redundancy: 1.9 % / CC1/2: 0.942 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.899→2.95 Å / Num. unique obs: 4309 / CC1/2: 0.745 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UZ9 Resolution: 2.899→14.996 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 211.61 Å2 / Biso mean: 77.0071 Å2 / Biso min: 34.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.899→14.996 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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