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Yorodumi- PDB-3x1l: Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x1l | ||||||
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Title | Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA/DNA / RNA-recognition motif / RNA silencing / RNA binding / RNA BINDING PROTEIN-RNA-DNA complex | ||||||
Function / homology | Function and homology information defense response to virus / nucleotide binding / RNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus DSM 3638 (archaea) Archaeoglobus fulgidus DSM 4304 (archaea) Pyrococcus furiosus COM1 (archaea) synthetic (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å | ||||||
Authors | Osawa, T. / Numata, T. | ||||||
Citation | Journal: Mol.Cell / Year: 2015 Title: Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog. Authors: Osawa, T. / Inanaga, H. / Sato, C. / Numata, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x1l.cif.gz | 518.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x1l.ent.gz | 402.5 KB | Display | PDB format |
PDBx/mmJSON format | 3x1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x1l_validation.pdf.gz | 522.3 KB | Display | wwPDB validaton report |
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Full document | 3x1l_full_validation.pdf.gz | 537.2 KB | Display | |
Data in XML | 3x1l_validation.xml.gz | 79 KB | Display | |
Data in CIF | 3x1l_validation.cif.gz | 110.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/3x1l ftp://data.pdbj.org/pub/pdb/validation_reports/x1/3x1l | HTTPS FTP |
-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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-Components
-CRISPR system Cmr subunit ... , 3 types, 4 molecules ABFG
#1: Protein | Mass: 78226.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: cmr2, PF1129 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1S6 |
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#2: Protein | Mass: 36366.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: cmr3, PF1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1S7 |
#4: Protein | Mass: 17407.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Gene: AF_1861 / Production host: Escherichia coli (E. coli) / References: UniProt: O28417 |
-Protein , 2 types, 4 molecules CDEH
#3: Protein | Mass: 39865.824 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Gene: AF_1863 / Production host: Escherichia coli (E. coli) / References: UniProt: O28416 #5: Protein | | Mass: 40298.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Gene: AF_1861 / Production host: Escherichia coli (E. coli) / References: UniProt: O28418 |
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-RNA chain / DNA chain , 2 types, 2 molecules IJ
#6: RNA chain | Mass: 12604.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus COM1 (archaea) / References: GenBank: CP003685 |
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#7: DNA chain | Mass: 9451.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence is complementary to entity_id 6 / Source: (synth.) synthetic (others) |
-Non-polymers , 3 types, 132 molecules
#8: Chemical | ChemComp-ZN / |
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#9: Chemical | ChemComp-MG / |
#10: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 13-15% (w/v) PEG 3350, 100mM succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.096→50 Å / Num. obs: 148845 / % possible obs: 97.4 % |
Reflection shell | Resolution: 2.1→2.22 Å / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.096→44.338 Å / SU ML: 0.24 / σ(F): 1.93 / Phase error: 27.43 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.096→44.338 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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