+Open data
-Basic information
Entry | Database: PDB / ID: 1llr | ||||||
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Title | CHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0012 | ||||||
Components | CHOLERA TOXIN B SUBUNIT | ||||||
Keywords | TOXIN / ENTEROTOXIN / RECEPTOR / B-PENTAMER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.46 Å | ||||||
Authors | Merritt, E.A. / Hol, W.G.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2002 Title: Characterization and crystal structure of a high-affinity pentavalent receptor-binding inhibitor for cholera toxin and E. coli heat-labile enterotoxin. Authors: Merritt, E.A. / Zhang, Z. / Pickens, J.C. / Ahn, M. / Hol, W.G. / Fan, E. | ||||||
History |
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Remark 600 | HETEROGEN Ligand BMS-0012 is a pentavalent ligand consisting of a pentacyclen core to which are ...HETEROGEN Ligand BMS-0012 is a pentavalent ligand consisting of a pentacyclen core to which are linked five long arms, each containing two 'linker' moities and terminating in a 'finger' derived from metanitrophenylgalactoside. For refinement the ligand was broken into pieces: FNG (for 'finger') is derived from metanitrophenyl-alpha-D-galactopyranoside. LNQ (for 'linker') is a linker group present in two copies per arm, only one of which is included in the model. There is an additional pentane-2-one which links the LNQ to the core. COR (for 'core', 1,4,7,10,13pentaaza-cyclopentadecane) is not present in this PDB file because it was not sufficiently well ordered to be included in the structural model. The central core of the ligand is inferred to lie near the central pore of the pentameric protein. Water numbering retained from 3CHB except that canonical sites (formerly 7000) are given the following numbers: 001-009 canonical waters at binding site of chain D 101-109 canonical waters at binding site of chain E 201-209 canonical waters at binding site of chain F 301-309 canonical waters at binding site of chain G 401-409 canonical waters at binding site of chain H All other waters (formerly 9000) given residue numbers 1001-1733. | ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1llr.cif.gz | 238.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1llr.ent.gz | 197.6 KB | Display | PDB format |
PDBx/mmJSON format | 1llr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1llr_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 1llr_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 1llr_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 1llr_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/1llr ftp://data.pdbj.org/pub/pdb/validation_reports/ll/1llr | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11623.267 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CTXB / Production host: Escherichia coli (E. coli) / References: GenBank: 48890, UniProt: Q57193*PLUS #2: Sugar | ChemComp-FNG / #3: Chemical | ChemComp-LNQ / #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: 2.18 Å3/Da / Density % sol: 43.64 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 300, NACL, MGCL2, TRIS HCL, pH 7.50, VAPOR DIFFUSION, SITTING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 11, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. all: 84902 / Num. obs: 84902 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.46→1.51 Å / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2 / % possible all: 81 |
Reflection | *PLUS Highest resolution: 1.46 Å / Lowest resolution: 50 Å / % possible obs: 97 % / Redundancy: 4 % |
Reflection shell | *PLUS % possible obs: 82 % / Num. unique obs: 7083 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Resolution: 1.46→27 Å / Cor.coef. Fo:Fc: 0.96029 / Cor.coef. Fo:Fc free: 0.94911 / SU B: 1.17719 / SU ML: 0.04407 / SU R Cruickshank DPI: 0.0805 / SU Rfree: 0.07012 / Cross valid method: RFREE / ESU R: 0.08 / ESU R Free: 0.07 Details: Protein + FNG residues refined with anisotropic Uij. Remainder of ligand atoms in model refined with isotropic U.
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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: Babinet model plus mask | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→27 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Highest resolution: 1.46 Å / Lowest resolution: 27 Å / Rfactor Rfree: 0.191 / Rfactor Rwork: 0.149 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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