+Open data
-Basic information
Entry | Database: PDB / ID: 3qjl | ||||||
---|---|---|---|---|---|---|---|
Title | One RAMP protein binding different RNA substrates | ||||||
Components |
| ||||||
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: 2.7009 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3qjl.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3qjl.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/3qjl ftp://data.pdbj.org/pub/pdb/validation_reports/qj/3qjl | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28067.678 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0350 / References: UniProt: O58088 #2: RNA chain | Mass: 3844.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CRISPR #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.07 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.005 M MgSO4, 0.05 M MES (pH6.0), 3-8% PEG4000, 0.2 M NaCl and 0.1 M KCl, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5621 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5621 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 28452 / Num. obs: 28452 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.7→50 Å / % possible all: 89 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7009→39.7 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 29.12 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.466 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7009→39.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|