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Yorodumi- PDB-3ec6: Crystal structure of the General Stress Protein 26 from Bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ec6 | ||||||
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Title | Crystal structure of the General Stress Protein 26 from Bacillus anthracis str. Sterne | ||||||
Components | General stress protein 26 | ||||||
Keywords | Structural Genomics / Unknown Function / alpha-beta structure / structural genomics of NIAID / Structural Genomics of National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Kim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the general stress protein 26 from Bacillus anthracis str. Sterne Authors: Kim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ec6.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ec6.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 3ec6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ec6_validation.pdf.gz | 752.4 KB | Display | wwPDB validaton report |
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Full document | 3ec6_full_validation.pdf.gz | 755.8 KB | Display | |
Data in XML | 3ec6_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 3ec6_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/3ec6 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/3ec6 | HTTPS FTP |
-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: 16288.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q81Z55, UniProt: A0A6L8PEJ3*PLUS |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | THE CODE IDP01540 DOES NOT EXIST IN TARGETDB AT THE TIME OF PROCESSING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.2 Details: 0.1M Hampton PH9.2, 2.8M NH4SO4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Apr 19, 2008 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→41.27 Å / Num. all: 16512 / Num. obs: 16512 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.02 Å2 / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.5 / Num. unique all: 608 / % possible all: 71.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→26.32 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.78 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.108 / ESU R Free: 0.108 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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 mean: 16.335 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→26.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.643 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -3.2248 Å / Origin y: 36.7979 Å / Origin z: 20.3917 Å
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