+Open data
-Basic information
Entry | Database: PDB / ID: 3pf4 | ||||||
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Title | Crystal structure of Bs-CspB in complex with r(GUCUUUA) | ||||||
Components |
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Keywords | GENE REGULATION/RNA / BETA BARREL / PROTEIN-RNA complex / COLD SHOCK RESPONSE / TRANSCRIPTION REGULATION / TRANSLATION REGULATION / OB fold / cold shock domain / RNA/DNA binding / single-stranded RNA and DNA / cytosol / GENE REGULATION-RNA complex | ||||||
Function / homology | Function and homology information nucleoid / regulation of gene expression / nucleic acid binding / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å | ||||||
Authors | Sachs, R. / Max, K.E.A. / Heinemann, U. | ||||||
Citation | Journal: Rna / Year: 2012 Title: RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution. Authors: Sachs, R. / Max, K.E. / Heinemann, U. / Balbach, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pf4.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pf4.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/3pf4 ftp://data.pdbj.org/pub/pdb/validation_reports/pf/3pf4 | HTTPS FTP |
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-Related structure data
Related structure data | 3pf5C 1cspS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 7372.126 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU09100, cspA, cspB / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P32081 #2: RNA chain | | Mass: 2159.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-MG / | #5: 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: 2.13 Å3/Da / Density % sol: 42.19 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: protein buffer: 50mM TRIS, 20mM Na-HEPES, pH 7.5; Bs-CspB.rGUCUUUA complex concentration: 50mg/ml; crystallization buffer: 30% (w/v) PEG 4000, 0.2M MgCl2, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, ...Details: protein buffer: 50mM TRIS, 20mM Na-HEPES, pH 7.5; Bs-CspB.rGUCUUUA complex concentration: 50mg/ml; crystallization buffer: 30% (w/v) PEG 4000, 0.2M MgCl2, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 20, 2009 Details: mirrors double crystal monochromator (Si-111 crystals) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si-(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.38→19.02 Å / Num. all: 30207 / Num. obs: 30207 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.74 % / Biso Wilson estimate: 22.784 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.73 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CSP Resolution: 1.38→19.02 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.149 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.884 / SU B: 2.077 / SU ML: 0.038 / SU R Cruickshank DPI: 0.063 / SU Rfree: 0.06 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.75 Å2 / Biso mean: 22.247 Å2 / Biso min: 9.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.167 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→19.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.38→1.416 Å / Total num. of bins used: 20
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