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Yorodumi- PDB-4j42: The crystal structure of a secreted protein EsxB (Mutant Y65F) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j42 | ||||||
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Title | The crystal structure of a secreted protein EsxB (Mutant Y65F) from Bacillus anthracis str. Sterne | ||||||
Components | secreted protein EsxBSecretion | ||||||
Keywords | UNKNOWN FUNCTION / structural genomics / PSI-Biology / protein structure initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information HP0062-like domain superfamily / HP0062-like domain / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / Helix Hairpins / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Fan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a secreted protein EsxB (Mutant Y65F) from Bacillus anthracis str. Sterne Authors: Fan, Y. / Tan, K. / Chhor, G. / 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 | 4j42.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j42.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 4j42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/4j42 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/4j42 | HTTPS FTP |
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-Related structure data
Related structure data | 4iyiS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10356.526 Da / Num. of mol.: 2 / Mutation: Y65F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: Bacillus anthracis, BAS2036, BA_2191, GBAA_2191 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81R67, UniProt: A0A6L7HJC4*PLUS #2: Chemical | ChemComp-FLC / | #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: 2.89 Å3/Da / Density % sol: 57.44 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Bis-Tris propane, 2M di-ammonium hydrogen citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-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 315r / Detector: CCD / Date: Apr 4, 2011 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→34 Å / Num. all: 61931 / Num. obs: 61931 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 40.7 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3054 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4IYI Resolution: 1.28→33.619 Å / SU ML: 0.1 / σ(F): 1.35 / Phase error: 16.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→33.619 Å
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Refine LS restraints |
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LS refinement shell |
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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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