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Yorodumi- PDB-3twi: Variable Lymphocyte Receptor Recognition of the Immunodominant Gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3twi | ||||||
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Title | Variable Lymphocyte Receptor Recognition of the Immunodominant Glycoprotein of Bacillus anthracis Spores | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Leucine-Rich Repeat / Antigen-binding / Secreted | ||||||
Function / homology | Function and homology information extracellular matrix structural constituent conferring tensile strength / regulation of phagocytosis / extracellular matrix organization / extracellular space Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) Petromyzon marinus (sea lamprey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Kirchdoerfer, R.N. / Herrin, B.R. / Han, B.W. / Turnbough Jr., C.L. / Cooper, M.D. / Wilson, I.A. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Variable Lymphocyte Receptor Recognition of the Immunodominant Glycoprotein of Bacillus anthracis Spores. Authors: Kirchdoerfer, R.N. / Herrin, B.R. / Han, B.W. / Turnbough, C.L. / Cooper, M.D. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3twi.cif.gz | 340.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3twi.ent.gz | 279.2 KB | Display | PDB format |
PDBx/mmJSON format | 3twi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3twi_validation.pdf.gz | 479.1 KB | Display | wwPDB validaton report |
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Full document | 3twi_full_validation.pdf.gz | 489.3 KB | Display | |
Data in XML | 3twi_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 3twi_validation.cif.gz | 49.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/3twi ftp://data.pdbj.org/pub/pdb/validation_reports/tw/3twi | HTTPS FTP |
-Related structure data
Related structure data | 3tyjC 2r6qS 2r9uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 85 - 210 / Label seq-ID: 26 - 151
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-Components
#1: Protein | Mass: 16422.553 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN / Mutation: T185N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: bclA, BA_1222, GBAA_1222 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81JD7 #2: Protein | Mass: 19471.273 Da / Num. of mol.: 3 / Fragment: ANTIGEN-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Gene: VLR-B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A9Z0I5 #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: 2.67 Å3/Da / Density % sol: 53.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.26 Details: 15% PEG 6000, 1.2 M LiCl, 0.1 M sodium citrate, pH 5.26, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2010 |
Radiation | Monochromator: Si(111), Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. all: 37042 / Num. obs: 37042 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rsym value: 0.122 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.581 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2R6Q, 2R9U Resolution: 2.55→41.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 19.502 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.267 / 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 mean: 35.948 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→41.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1424 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.55→2.613 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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