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Yorodumi- PDB-3dnp: Crystal structure of Stress response protein yhaX from Bacillus s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dnp | ||||||
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Title | Crystal structure of Stress response protein yhaX from Bacillus subtilis | ||||||
Components | Stress response protein yhaXFight-or-flight response | ||||||
Keywords | structural genomics / unknown function / Stress response protein yhaX / Bacillus subtilis / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Stress response | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å | ||||||
Authors | Chang, C. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Stress response protein yhaX from Bacillus subtilis Authors: Chang, C. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dnp.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dnp.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/3dnp ftp://data.pdbj.org/pub/pdb/validation_reports/dn/3dnp | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-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: 33050.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yhaX, BSU09830 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star / References: UniProt: O07539 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-EDO / |
#4: 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: 2.5 Å3/Da / Density % sol: 50.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50mM MgCl2, 0.1 M HEPES pH 7.5, 30% PEGMME 550, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2008 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 29564 / Num. obs: 29455 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.096 / Χ2: 2.9 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.85→1.87 Å / Redundancy: 10 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 3.48 / Num. unique all: 713 / Χ2: 1.506 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.894 / SU B: 4.501 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.119 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.75 Å2 / Biso mean: 29.093 Å2 / Biso min: 9.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.851→1.899 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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