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Yorodumi- PDB-5lzh: Cholera toxin classical B-pentamer in complex with inhibitor PC262 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lzh | |||||||||
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Title | Cholera toxin classical B-pentamer in complex with inhibitor PC262 | |||||||||
Components | (Cholera enterotoxin B ...) x 2 | |||||||||
Keywords | TOXIN / cholera toxin B-pentamer / inhibitor | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å | |||||||||
Authors | Heggelund, J.E. / Martinsen, T. / Krengel, U. | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics. Authors: Heggelund, J.E. / Mackenzie, A. / Martinsen, T. / Benjamin Heim, J. / Cheshev, P. / Bernardi, A. / Krengel, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lzh.cif.gz | 238.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lzh.ent.gz | 192.9 KB | Display | PDB format |
PDBx/mmJSON format | 5lzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lzh_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5lzh_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5lzh_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 5lzh_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/5lzh ftp://data.pdbj.org/pub/pdb/validation_reports/lz/5lzh | HTTPS FTP |
-Related structure data
Related structure data | 5lzgC 5lziC 5lzjC 3chbS 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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-Components
-Cholera enterotoxin B ... , 2 types, 5 molecules ABDCE
#1: Protein | Mass: 11655.267 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Gene: ctxB, EN12_07055, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003, ERS013207_03244 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57193 #2: Protein | Mass: 11623.267 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Gene: ctxB, EN12_07055, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003, ERS013207_03244 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57193 |
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-Non-polymers , 6 types, 619 molecules
#3: Chemical | ChemComp-7BN / ( #4: Chemical | ChemComp-MRD / ( | #5: Chemical | #6: Chemical | ChemComp-TRS / | #7: Chemical | ChemComp-PEG / | #8: 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: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES/Imidazole pH 6.5, 8% PEG1000, 8% PEG 3350, 8% MPD, 0.03 M divalent cations |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.991872 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.991872 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→49 Å / Num. obs: 135800 / % possible obs: 73.7 % / Redundancy: 2.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.87 |
Reflection shell | Resolution: 1.13→1.19 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 0.73 / CC1/2: 0.504 / % possible all: 13.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CHB Resolution: 1.13→73.55 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.685 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.058 / 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: 17.606 Å2
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Refinement step | Cycle: 1 / Resolution: 1.13→73.55 Å
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Refine LS restraints |
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