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Yorodumi- PDB-2nrj: Crystal Structure of Hemolysin binding component from Bacillus cereus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nrj | ||||||
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Title | Crystal Structure of Hemolysin binding component from Bacillus cereus | ||||||
Components | Hbl B protein | ||||||
Keywords | TOXIN / Enterotoxin / Hemolysis / Transmembrane / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information hemolysis in another organism / : / toxin activity / membrane => GO:0016020 / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å | ||||||
Authors | Madegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2008 Title: X-ray crystal structure of the B component of Hemolysin BL from Bacillus cereus Authors: Madegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nrj.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nrj.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 2nrj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nrj_validation.pdf.gz | 425.9 KB | Display | wwPDB validaton report |
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Full document | 2nrj_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 2nrj_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 2nrj_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/2nrj ftp://data.pdbj.org/pub/pdb/validation_reports/nr/2nrj | 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: 38934.703 Da / Num. of mol.: 1 / Fragment: residues 32-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: hblA / Plasmid: pSGX4 (BS) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)+Codon+RIL / References: UniProt: Q9REG6, UniProt: P80172*PLUS |
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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: 2.03 Å3/Da / Density % sol: 39.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG 4000, 0.2M Magnesium Chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9772 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9772 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→26.05 Å / Num. all: 20797 / Num. obs: 20797 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.272 / Num. unique all: 1974 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.03→26.05 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 92972.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The authors state that the missing residues listed in remark 465 are due to lack of electron density
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.8406 Å2 / ksol: 0.368405 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→26.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.16 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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