+Open data
-Basic information
Entry | Database: PDB / ID: 3wbm | ||||||
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Title | Crystal Structure of protein-RNA complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / PROTEIN-RNA COMPLEX / DNA/RNA BINDING / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information chromosome condensation / chromosome / double-stranded DNA binding / Hydrolases; Acting on ester bonds / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus shibatae (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ding, J. / Wang, D.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Biochemical and structural insights into RNA binding by Ssh10b, a member of the highly conserved Sac10b protein family in Archaea. Authors: Guo, L. / Ding, J. / Guo, R. / Hou, Y. / Wang, D.C. / Huang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wbm.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wbm.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/3wbm ftp://data.pdbj.org/pub/pdb/validation_reports/wb/3wbm | HTTPS FTP |
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-Related structure data
Related structure data | 1h0xS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 10601.442 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus shibatae (archaea) / Strain: 2286 / Gene: albA1, ssh10b / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60848 #2: RNA chain | Mass: 7949.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: 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: 2.43 Å3/Da / Density % sol: 49.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 18% (v/v) PEG 5000 MME, 100mM Bis-Tris, 200mM sodium malonate, 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: 0.9642 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9642 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.84 Å / Num. all: 37892 / Num. obs: 37589 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 18.85 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5444 / Rsym value: 0.407 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H0X Resolution: 2→43.804 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8165 / SU ML: 0.23 / σ(F): 1.35 / Phase error: 25.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.773 Å2 / ksol: 0.351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.96 Å2 / Biso mean: 40.5243 Å2 / Biso min: 14.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.804 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: 13
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