+Open data
-Basic information
Entry | Database: PDB / ID: 3qjp | ||||||
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Title | An RAMP protein binding different RNA substrates | ||||||
Components |
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Keywords | IMMUNE SYSTEM/RNA / Ferridoxin-fold / work in immune system in prokaryotes / IMMUNE SYSTEM-RNA complex | ||||||
Function / homology | Function and homology information hydrolase activity, acting on ester bonds / defense response to virus / RNA binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2986 Å | ||||||
Authors | Wang, R. / Zheng, H. / Preamplume, G. / Li, H. | ||||||
Citation | Journal: To be Published Title: Cooperative and Specific Binding of a RAMP Protein to Single-stranded CRISPR Repeat RNA Authors: Wang, R. / Zheng, H. / Preamplume, G. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qjp.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qjp.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qjp_validation.pdf.gz | 456.1 KB | Display | wwPDB validaton report |
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Full document | 3qjp_full_validation.pdf.gz | 475 KB | Display | |
Data in XML | 3qjp_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3qjp_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/3qjp ftp://data.pdbj.org/pub/pdb/validation_reports/qj/3qjp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 2512.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CRISPR |
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#2: Protein | Mass: 27929.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0350 / References: UniProt: O58088 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.68 Å3/Da / Density % sol: 73.71 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.01 M MgSO4, 0.05 M Na Cacodylate (pH6.0), and 1.8 M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5621 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5621 Å / Relative weight: 1 |
Reflection | Resolution: 3.2986→50 Å / Num. all: 9254 / Num. obs: 9254 / % possible obs: 83 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_589) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2986→30.295 Å / SU ML: 0.45 / σ(F): 0 / Phase error: 26.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.24 Å2 / ksol: 0.297 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.2986→30.295 Å
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Refine LS restraints |
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LS refinement shell |
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