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Yorodumi- PDB-3g1b: The structure of the M53A mutant of Caulobacter crescentus clpS p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g1b | ||||||
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Title | The structure of the M53A mutant of Caulobacter crescentus clpS protease adaptor protein in complex with WLFVQRDSKE peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / adaptor / protein-peptide complex / peptide-binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Caulobacter vibrioides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.448 Å | ||||||
Authors | Baker, T.A. / Roman-Hernandez, G. / Sauer, R.T. / Grant, R.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Molecular basis of substrate selection by the N-end rule adaptor protein ClpS. Authors: Roman-Hernandez, G. / Grant, R.A. / Sauer, R.T. / Baker, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g1b.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g1b.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 3g1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/3g1b ftp://data.pdbj.org/pub/pdb/validation_reports/g1/3g1b | HTTPS FTP |
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-Related structure data
Related structure data | 3g19C 3gq0C 3gq1C 3gw1C 3dnjS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 9884.229 Da / Num. of mol.: 2 / Mutation: M53A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: CB15 / Gene: CC_2467, clpS / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A5I0 #2: Protein/peptide | Mass: 1309.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide #3: Chemical | #4: 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: 1.7045 Å3/Da / Density % sol: 27.838091 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 5.5 Details: 0.1 M bis-tris pH 5.5, 0.2 M MgCl2, 20% PEG 3350, VAPOR DIFFUSION, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 17, 2008 / Details: varimax-hr | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Varimax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→100 Å / Num. obs: 23780 / % possible obs: 88.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.057 / Χ2: 1.125 / Net I/σ(I): 34.292 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Starting model: 3dnj Resolution: 1.448→22.725 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.885 / SU ML: 0.12 / σ(F): 1.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.262 Å2 / ksol: 0.459 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.02 Å2 / Biso mean: 19.862 Å2 / Biso min: 9.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.448→22.725 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: 14
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