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- PDB-1g8z: HIS57ALA MUTANT OF CHOLERA TOXIN B-PENATMER -

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Basic information

Entry
Database: PDB / ID: 1g8z
TitleHIS57ALA MUTANT OF CHOLERA TOXIN B-PENATMER
ComponentsCHOLERA TOXIN B PROTEIN
KeywordsTOXIN
Function / homology
Function and homology information


host cell surface binding / galactose binding / catalytic complex / positive regulation of tyrosine phosphorylation of STAT protein / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAman, A.T. / Fraser, S. / Merritt, E.A. / Rodigherio, C. / Kenny, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: A mutant cholera toxin B subunit that binds GM1- ganglioside but lacks immunomodulatory or toxic activity.
Authors: Aman, A.T. / Fraser, S. / Merritt, E.A. / Rodigherio, C. / Kenny, M. / Ahn, M. / Hol, W.G. / Williams, N.A. / Lencer, W.I. / Hirst, T.R.
History
DepositionNov 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: CHOLERA TOXIN B PROTEIN
E: CHOLERA TOXIN B PROTEIN
F: CHOLERA TOXIN B PROTEIN
G: CHOLERA TOXIN B PROTEIN
H: CHOLERA TOXIN B PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5029
Polymers57,7815
Non-polymers7214
Water8,035446
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.362, 114.722, 45.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
CHOLERA TOXIN B PROTEIN / CTB


Mass: 11556.197 Da / Num. of mol.: 5 / Mutation: H57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CTXB / Production host: Escherichia coli (E. coli) / References: UniProt: P01556
#2: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG 5000, NaCl, Tris HCl, galactose, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM1reservoirNaCl
2100 mMTris-HCl1reservoir
332 %(w/v)PEG50001reservoir
43 mg/mlprotein1drop
5100 mMTris-HCl1drop
6300 mMbeta-D-galactopyranoside1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→22 Å / Num. all: 36777 / Num. obs: 36777 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 37
Reflection shellResolution: 2→2.07 Å / Redundancy: 6 % / Rmerge(I) obs: 0.16 / Num. unique all: 3632 / % possible all: 99.3
Reflection
*PLUS

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_4.0.0 01/12/1999refinement
d*TREKdata reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.551 / SU ML: 0.103 / SU R Cruickshank DPI: 0.191 / SU Rfree: 0.176 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1827 4.991 %RANDOM
Rwork0.179 ---
all-36607 --
obs-34780 --
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 48 446 4539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONp_bond_d0.0110.024163
X-RAY DIFFRACTIONp_angle_d0.030.045638
X-RAY DIFFRACTIONp_planar_d0.0320.051320
X-RAY DIFFRACTIONp_plane_restr0.0030.023485
X-RAY DIFFRACTIONp_chiral_restr0.1110.15666
X-RAY DIFFRACTIONp_singtor_nbd0.1760.31563
X-RAY DIFFRACTIONp_multtor_nbd0.2460.32205
X-RAY DIFFRACTIONp_xyhbond_nbd0.1360.3146
X-RAY DIFFRACTIONp_planar_tor3.967525
X-RAY DIFFRACTIONp_staggered_tor14.89815775
X-RAY DIFFRACTIONp_orthonormal_tor30.4582050
X-RAY DIFFRACTIONp_mcbond_it2.96222303
X-RAY DIFFRACTIONp_mcangle_it3.89132773
X-RAY DIFFRACTIONp_scbond_it3.83321860
X-RAY DIFFRACTIONp_scangle_it5.28832865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection all
2-2.09430.222210.1534404X-RAY DIFFRACTION4666
2.094-2.19780.2312240.1424011X-RAY DIFFRACTION4244
2.198-2.31220.2151920.1453671X-RAY DIFFRACTION3874
2.312-2.43910.2441700.1453282X-RAY DIFFRACTION3456
2.439-2.58070.2081460.152987X-RAY DIFFRACTION3134
2.581-2.73980.2511460.1612662X-RAY DIFFRACTION2813
2.74-2.91980.2341180.1612338X-RAY DIFFRACTION2456
2.92-3.12510.2981110.1672080X-RAY DIFFRACTION2191
3.125-3.36140.255910.1791804X-RAY DIFFRACTION1897
3.361-3.63640.219790.1791567X-RAY DIFFRACTION1646
3.636-3.96050.178650.1821346X-RAY DIFFRACTION1411
3.96-4.34790.187620.1841110X-RAY DIFFRACTION1172
4.348-4.81940.184540.195932X-RAY DIFFRACTION986
4.819-5.40550.299470.219750X-RAY DIFFRACTION797
5.405-6.15390.312360.288595X-RAY DIFFRACTION633
6.154-7.1430.457240.34456X-RAY DIFFRACTION481
7.143-8.51070.438240.35337X-RAY DIFFRACTION366
8.511-10.52640.2990.418223X-RAY DIFFRACTION249
10.526-13.79320.50170.399144X-RAY DIFFRACTION163
13.793-200.20510.40881X-RAY DIFFRACTION94
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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