+Open data
-Basic information
Entry | Database: PDB / ID: 1qoh | ||||||
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Title | A MUTANT SHIGA-LIKE TOXIN IIE | ||||||
Components | SHIGA-LIKE TOXIN IIE B SUBUNIT | ||||||
Keywords | TOXIN / RECEPTOR BINDING / PROTEIN-CARBOHYDRATE RECOGNITION / SPECIFICITY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Pannu, N.S. / Boodhoo, A. / Armstrong, G.D. / Clark, C.G. / Brunton, J.L. / Read, R.J. | ||||||
Citation | Journal: Structure / Year: 2000 Title: A Mutant Shiga-Like Toxin Iie Bound to its Receptor Gb(3): Structure of a Group II Shiga-Like Toxin with Altered Binding Specificity Authors: Ling, H. / Pannu, N.S. / Boodhoo, A. / Armstrong, G.D. / Clark, C.G. / 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. #2: Journal: Nature / Year: 1992 Title: Crystal Structure of the Cell-Binding B Oligomer of Verotoxin-1 from E. Coli Authors: Stein, P.E. / Boodhoo, A. / Tyrrell, G.J. / 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 | 1qoh.cif.gz | 274 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qoh.ent.gz | 224.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qoh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/1qoh ftp://data.pdbj.org/pub/pdb/validation_reports/qo/1qoh | HTTPS FTP |
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-Related structure data
Related structure data | 2bosSC 1bov 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THERE ARE FOUR PENTAMERS PER ASYMMETRIC UNIT |
-Components
#1: Protein | Mass: 7590.411 Da / Num. of mol.: 20 / Fragment: RECEPTOR-BINDING DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH PK-MCO, AN ANALOGUE OF GB3 (GLOBOTRIAOSYL CERAMIDE) Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47644 #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: 2.25 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: 8% PEG8000, 0.1M NACL, 0.1M IMIDAZOLE, PH=7.4, pH 7.40 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 15, 1993 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20.36 Å / Num. obs: 34188 / % possible obs: 60.1 % / Observed criterion σ(I): 0 / Redundancy: 1.83 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.0844 / Rsym value: 0.0844 / Net I/σ(I): 8.415 |
Reflection shell | Resolution: 2.35→2.49 Å / Redundancy: 1.66 % / Rmerge(I) obs: 0.3296 / Mean I/σ(I) obs: 0.968 / Rsym value: 0.3296 / % possible all: 24.9 |
Reflection | *PLUS Num. measured all: 62524 |
Reflection shell | *PLUS % possible obs: 24.85 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BOV AND 2BOS Resolution: 2.35→21 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1888964.51 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.9572 Å2 / ksol: 0.296191 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→21 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 3.155 Å2 / Rms dev position: 0.153 Å / Weight Biso : 3.5 / Weight position: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.5 Å / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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