+Open data
-Basic information
Entry | Database: PDB / ID: 1c48 | ||||||
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Title | MUTATED SHIGA-LIKE TOXIN B SUBUNIT (G62T) | ||||||
Components | PROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT) | ||||||
Keywords | TOXIN / RECEPTOR BINDING / PROTEIN-CARBOHYDRATE RECOGNITION / OB-FOLD | ||||||
Function / homology | Function and homology information symbiont-mediated modulation of host virulence / hemolysis by symbiont of host erythrocytes / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Phage h30 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Ling, H. / Bast, D. / Brunton, J.L. / Read, R.J. | ||||||
Citation | Journal: To be Published Title: Identification of the Primary Receptor Binding Site of Shiga-Like Toxin B Subunits: Structures of Mutated Shiga-Like Toxin I B-Pentamer with and without Bound Carbohydrate Authors: Ling, H. / Bast, D. / Brunton, J.L. / Read, R.J. #1: Journal: Biochemistry / Year: 1998 Title: Structure of the Shiga-Like Toxin I B-Pentamer Complexed with an Analogue of its Receptor Gb3 Authors: Ling, H. / Boodhoo, A. / Hazes, B. / Cummings, M.D. / Armstrong, G.D. / Brunton, J.L. / Read, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c48.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c48.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 1c48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c48_validation.pdf.gz | 452.9 KB | Display | wwPDB validaton report |
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Full document | 1c48_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | 1c48_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1c48_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/1c48 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/1c48 | HTTPS FTP |
-Related structure data
Related structure data | 1c4qC 1bosS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 7742.686 Da / Num. of mol.: 5 / Fragment: RECEPTOR-BINDING DOMAIN / Mutation: G62T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phage h30 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P69178 #2: 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: 2.07 Å3/Da / Density % sol: 40.56 % |
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Crystal grow | pH: 8.5 / Details: pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978 |
Detector | Detector: CCD / Date: Mar 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→55 Å / Num. obs: 41266 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.6→1.65 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.305 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BOS Resolution: 1.6→55 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 47.07 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→55 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.65 Å / Total num. of bins used: 23
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Xplor file |
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