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- PDB-1c48: MUTATED SHIGA-LIKE TOXIN B SUBUNIT (G62T) -

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Basic information

Entry
Database: PDB / ID: 1c48
TitleMUTATED SHIGA-LIKE TOXIN B SUBUNIT (G62T)
ComponentsPROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT)
KeywordsTOXIN / RECEPTOR BINDING / PROTEIN-CARBOHYDRATE RECOGNITION / OB-FOLD
Function / homology
Function and homology information


modulation of host virulence by virus / hemolysis by symbiont of host erythrocytes / toxin activity / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Shiga-like toxin 1 subunit B
Similarity search - Component
Biological speciesPhage h30 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLing, 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
DepositionAug 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT)
B: PROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT)
C: PROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT)
D: PROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT)
E: PROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)38,7135
Polymers38,7135
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-36 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.972, 61.928, 60.327
Angle α, β, γ (deg.)90.00, 114.12, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.339709, -0.926657, -0.160949), (0.931875, 0.308455, 0.190956), (-0.127306, -0.214854, 0.968314)29.116, -39.9257, 4.8519
2given(-0.663922, -0.59307, -0.455496), (0.615463, -0.779338, 0.117636), (-0.424751, -0.20224, 0.882432)73.4746, -26.8361, 18.2715
3given(-0.643159, 0.561526, -0.520611), (-0.582412, -0.800127, -0.143503), (-0.497135, 0.210914, 0.841648)72.8158, 25.0657, 20.7311
4given(0.329328, 0.936505, -0.120421), (-0.930738, 0.300504, -0.208384), (-0.158966, 0.180707, 0.970605)28.1841, 40.248, 7.868

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Components

#1: Protein
PROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT)


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 / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorDetector: CCD / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.3Drefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOS

1bos


Resolution: 1.6→55 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1196 2.9 %THIN SHELLS
Rwork0.196 ---
obs0.196 41266 98.8 %-
Solvent computationBsol: 47.07 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-5.956 Å20 Å2-4.084 Å2
2--0.452 Å20 Å2
3----6.409 Å2
Refinement stepCycle: LAST / Resolution: 1.6→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 0 348 3127
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.82
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it3.132.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.6→1.65 Å / Total num. of bins used: 23
RfactorNum. reflection% reflection
Rfree0.337 334 1.03 %
Rwork0.32 3219 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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