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- PDB-1md2: CHOLERA TOXIN B-PENTAMER WITH DECAVALENT LIGAND BMSC-0013 -

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Basic information

Entry
Database: PDB / ID: 1md2
TitleCHOLERA TOXIN B-PENTAMER WITH DECAVALENT LIGAND BMSC-0013
ComponentsCHOLERA TOXIN B SUBUNIT
KeywordsTOXIN / multivalent inhibitor toxin
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
Chem-233 / CYANIDE ION / 3-ETHYLAMINO-4-METHYLAMINO-CYCLOBUTANE-1,2-DIONE / : / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous to 3CHB / Resolution: 1.45 Å
AuthorsZhang, Z. / Merritt, E.A. / Ahn, M. / Roach, C. / Hol, W.G.J. / Fan, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: Solution and crystallographic studies of branched multivalent ligands that inhibit the receptor-binding of cholera toxin.
Authors: Zhang, Z. / Merritt, E.A. / Ahn, M. / Roach, C. / Hou, Z. / Verlinde, C.L. / Hol, W.G. / Fan, E.
History
DepositionAug 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Remark 600HETEROGEN Ligand 233 (BMSC-0013) is a decavalent ligand consisting of a pentacyclen core to which ...HETEROGEN Ligand 233 (BMSC-0013) is a decavalent ligand consisting of a pentacyclen core to which are attached five long arms, each containing four 'linker' moieties followed by a squaric acid moiety and then branching to present two monovalent ligands derived from beta-D-galactose. A single copy of the decavalent ligand lies on a 2-fold and straddles two crystallographic asymmetric units. The central core and linker groups do not satisfy crystallographic symmetry and are not visible in the structure and hence not present in this model. The sulfur atom belongs to an unknown species (residue 109, chains D-H) constituting a partial- occupancy improperly formed cysteine disulfide between residues 9 and 86. That is, ~80% of the time there is a 9-86 disulfide and ~20% of the time there is a 9-??? disulfide.
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,36713
Polymers58,2775
Non-polymers2,0908
Water12,142674
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.124, 66.176, 78.221
Angle α, β, γ (deg.)90.00, 106.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-1208-

CYN

21F-1208-

CYN

DetailsThe crystallized complex contains two CTB pentamers sandwiching a single decavalent ligand. This sandwich spans 2 asymmetric units.

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Components

#1: Protein
CHOLERA TOXIN B SUBUNIT


Mass: 11655.332 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CTXB / Production host: Escherichia coli (E. coli) / References: GenBank: 48890, UniProt: P01556*PLUS
#2: Chemical
ChemComp-233 / [5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLCARBAMOYL)-PENTYL]-CARBAMIC ACID METHYL ESTER / BMSC-0013


Mass: 350.365 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H26N2O8
#3: Chemical ChemComp-SQ / 3-ETHYLAMINO-4-METHYLAMINO-CYCLOBUTANE-1,2-DIONE / SQUARIC ACID / Squaric acid


Mass: 156.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12N2O2 / Comment: inhibitor*YM
#4: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature rtK
Temp details: room temperature
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.0 mg/mlprotein1drop
2100 mMTris-HCl1droppH7.5
30.25 mMligand 121drop
450 mM1reservoirNaCl
5100 mMTris-HCl1reservoirpH7.5
640 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9789 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 84651 / Num. obs: 84651 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3176 / % possible all: 32
Reflection
*PLUS
Highest resolution: 1.45 Å / Lowest resolution: 50 Å / Num. obs: 81475 / % possible obs: 92 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Highest resolution: 1.45 Å / Lowest resolution: 1.51 Å / % possible obs: 54 % / Num. unique obs: 5338 / Rmerge(I) obs: 0.306

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
REFMACrefinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: isomorphous to 3CHB
Starting model: PDB entry 3CHB

3chb


Resolution: 1.45→25 Å / Cor.coef. Fo:Fc: 0.97049 / Cor.coef. Fo:Fc free: 0.95845 / σ(F): 0 / ESU R: 0.07416 / ESU R Free: 0.06325
RfactorNum. reflection
Rfree0.16432 4085
Rwork0.1252 -
all-77338
obs-77338
Refinement stepCycle: LAST / Resolution: 1.45→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 193 674 4967
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.035
X-RAY DIFFRACTIONp_bond_d0.019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.45-1.5220.2373310.18X-RAY DIFFRACTION64186
1.522-1.6010.1954820.138X-RAY DIFFRACTION85766
1.601-1.6890.164530.106X-RAY DIFFRACTION91706
1.689-1.7870.164280.093X-RAY DIFFRACTION82466
1.787-1.8970.1633840.087X-RAY DIFFRACTION73316
1.897-2.0210.1413560.092X-RAY DIFFRACTION64906
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.164 / Rfactor Rwork: 0.125
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.018

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