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Yorodumi- PDB-2z5w: tBclA, a recombinant spore surface protein from Bacillus anthracis -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z5w | ||||||
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Title | tBclA, a recombinant spore surface protein from Bacillus anthracis | ||||||
Components | BclA protein | ||||||
Keywords | STRUCTURAL PROTEIN / tBclA / JELLY-ROLL TOPOLOGY / Hypothetical protein | ||||||
Function / homology | Function and homology information Leader peptide, exosporium / BclA, C-terminal domain / BclA C-terminal domain / : / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Streltsov, V.A. | ||||||
Citation | Journal: BIOTECHNOL.BIOENG. / Year: 2008 Title: Construction, crystal structure and application of a recombinant protein that lacks the collagen-like region of BclA from Bacillus anthracis spores. Authors: Liu, C.Q. / Nuttall, S.D. / Tran, H. / Wilkins, M. / Streltsov, V.A. / Alderton, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z5w.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z5w.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 2z5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z5w_validation.pdf.gz | 375.5 KB | Display | wwPDB validaton report |
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Full document | 2z5w_full_validation.pdf.gz | 375.9 KB | Display | |
Data in XML | 2z5w_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 2z5w_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/2z5w ftp://data.pdbj.org/pub/pdb/validation_reports/z5/2z5w | HTTPS FTP |
-Related structure data
Related structure data | 1wckS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit |
-Components
#1: Protein | Mass: 13516.480 Da / Num. of mol.: 1 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne strain 34F2 / Gene: bclA / Plasmid: pFB45 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLacI / References: UniProt: Q83WA5, UniProt: Q83WA8*PLUS | ||
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#2: Chemical | #3: 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: 4.05 Å3/Da / Density % sol: 69.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES (pH 6.5), 17.5% EtOH, 5% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 138 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.96426 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96426 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→81.65 Å / Num. all: 43616 / Num. obs: 43616 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 33 % / Biso Wilson estimate: 16.86 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 74.9 |
Reflection shell | Resolution: 1.35→1.38 Å / Redundancy: 7 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1WCK Resolution: 1.35→47.82 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.677 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.043 / ESU R Free: 0.045 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→47.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.349→1.384 Å / Total num. of bins used: 20
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