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Yorodumi- PDB-2i5l: Crystal structure of Bacillus subtilis Cold Shock Protein variant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i5l | ||||||
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Title | Crystal structure of Bacillus subtilis Cold Shock Protein variant Bs-CspB M1R/E3K/K65I | ||||||
Components | Cold shock protein cspBCold shock response | ||||||
Keywords | GENE REGULATION / oligonucleotide/oligosaccharide binding fold / cold shock domain / beta-barrel / DNA binding protein / expression regulator | ||||||
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 / Resolution: 2.55 Å | ||||||
Authors | Max, K.E.A. / Heinemann, U. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Optimized variants of the cold shock protein from in vitro selection: structural basis of their high thermostability. Authors: Max, K.E. / Wunderlich, M. / Roske, Y. / Schmid, F.X. / Heinemann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i5l.cif.gz | 25.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i5l.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 2i5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/2i5l ftp://data.pdbj.org/pub/pdb/validation_reports/i5/2i5l | HTTPS FTP |
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-Related structure data
Related structure data | 2i5mC 1csqS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7382.168 Da / Num. of mol.: 1 / Mutation: M1R, E3K, K65I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: cspB, cspA / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P32081 |
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#2: 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: 2.89 Å3/Da / Density % sol: 57.48 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: protein solution: 20 mM TRIS pH 7.5, 50 mM sodium chloride, 3 mM magnesium chloride, 20.4 mg/ml protein. crystallization buffer: 25 % PEG 3350, 0.2 M sodium carbonate, 0.1 M TRIS HCl pH 8.5. ...Details: protein solution: 20 mM TRIS pH 7.5, 50 mM sodium chloride, 3 mM magnesium chloride, 20.4 mg/ml protein. crystallization buffer: 25 % PEG 3350, 0.2 M sodium carbonate, 0.1 M TRIS HCl pH 8.5. crystallization setup: 0.8 microliter protein solution:0.8 microliter reservoir solution, 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: 0.9537 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 18, 2005 / Details: mirrors |
Radiation | Monochromator: double-crystal monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.2 Å / Num. all: 3258 / Num. obs: 3223 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 9.72 % / Biso Wilson estimate: 49.578 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 20.14 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 9.36 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.8 / Num. measured obs: 3288 / Num. unique all: 351 / % possible all: 98.6 |
-Phasing
Phasing MR | Rfactor: 0.382 / Cor.coef. Fo:Fc: 0.684 / Cor.coef. Io to Ic: 0.717
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1CSQ Resolution: 2.55→18.5 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / SU B: 9.525 / SU ML: 0.2 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.485 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.449 Å2
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Refine analyze | Luzzati coordinate error free: 0.27 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→18.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Total num. of bins used: 20
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