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- PDB-1jqy: HEAT-LABILE ENTEROTOXIN B-PENTAMER WITH LIGAND BMSC-0010 -

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Basic information

Entry
Database: PDB / ID: 1jqy
TitleHEAT-LABILE ENTEROTOXIN B-PENTAMER WITH LIGAND BMSC-0010
ComponentsHEAT-LABILE ENTEROTOXIN B CHAIN
KeywordsTOXIN / ENTEROTOXIN / RECEPTOR / LIGAND / B-PENTAMER
Function / homology
Function and homology information


toxin activity / killing of cells of another organism / extracellular region
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-A32 / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.14 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
CitationJournal: Chem.Biol. / Year: 2002
Title: Anchor-based design of improved cholera toxin and E. coli heat-labile enterotoxin receptor binding antagonists that display multiple binding modes.
Authors: Pickens, J.C. / Merritt, E.A. / Ahn, M. / Verlinde, C.L. / Hol, W.G. / Fan, E.
History
DepositionAug 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: HEAT-LABILE ENTEROTOXIN B CHAIN
E: HEAT-LABILE ENTEROTOXIN B CHAIN
F: HEAT-LABILE ENTEROTOXIN B CHAIN
G: HEAT-LABILE ENTEROTOXIN B CHAIN
H: HEAT-LABILE ENTEROTOXIN B CHAIN
L: HEAT-LABILE ENTEROTOXIN B CHAIN
M: HEAT-LABILE ENTEROTOXIN B CHAIN
N: HEAT-LABILE ENTEROTOXIN B CHAIN
O: HEAT-LABILE ENTEROTOXIN B CHAIN
P: HEAT-LABILE ENTEROTOXIN B CHAIN
V: HEAT-LABILE ENTEROTOXIN B CHAIN
W: HEAT-LABILE ENTEROTOXIN B CHAIN
X: HEAT-LABILE ENTEROTOXIN B CHAIN
Y: HEAT-LABILE ENTEROTOXIN B CHAIN
Z: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,71329
Polymers177,11315
Non-polymers6,60014
Water19,4921082
1
D: HEAT-LABILE ENTEROTOXIN B CHAIN
E: HEAT-LABILE ENTEROTOXIN B CHAIN
F: HEAT-LABILE ENTEROTOXIN B CHAIN
G: HEAT-LABILE ENTEROTOXIN B CHAIN
H: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,39510
Polymers59,0385
Non-polymers2,3575
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16690 Å2
ΔGint-61 kcal/mol
Surface area19860 Å2
MethodPISA
2
L: HEAT-LABILE ENTEROTOXIN B CHAIN
M: HEAT-LABILE ENTEROTOXIN B CHAIN
N: HEAT-LABILE ENTEROTOXIN B CHAIN
O: HEAT-LABILE ENTEROTOXIN B CHAIN
P: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9249
Polymers59,0385
Non-polymers1,8864
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16990 Å2
ΔGint-57 kcal/mol
Surface area20040 Å2
MethodPISA
3
V: HEAT-LABILE ENTEROTOXIN B CHAIN
W: HEAT-LABILE ENTEROTOXIN B CHAIN
X: HEAT-LABILE ENTEROTOXIN B CHAIN
Y: HEAT-LABILE ENTEROTOXIN B CHAIN
Z: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,39510
Polymers59,0385
Non-polymers2,3575
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17170 Å2
ΔGint-62 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.990, 166.006, 74.420
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HEAT-LABILE ENTEROTOXIN B CHAIN


Mass: 11807.539 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ETXB / Plasmid: PROFIT / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P32890
#2: Chemical
ChemComp-A32 / (3-NITRO-5-(3-MORPHOLIN-4-YL-PROPYLAMINOCARBONYL)PHENYL)-GALACTOPYRANOSIDE / BMSC-0010


Mass: 471.458 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C20H29N3O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1082 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3000, NaCl, Tris HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.0 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
3200 mM1dropNaCl
43 mM1dropNaN3
51 mMEDTA1drop
650 mM1reservoirNaCl
7100 mMTris-HCl1reservoirpH6.5
830 %PEG30001reservoir

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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 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.14→82 Å / Num. all: 84223 / Num. obs: 84223 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 4 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 5.5 / Num. unique all: 7200 / % possible all: 83.3
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 97 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 83 %

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Processing

Software
NameVersionClassification
d*TREKdata scaling
SCALEPACKdata scaling
TRUNCATEdata reduction
AMoREphasing
REFMACrefinement
d*TREKdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.14→25 Å / Cor.coef. Fo:Fc: 0.921 / SU B: 8.061 / SU ML: 0.21 / σ(F): 0 / ESU R: 0.35 / ESU R Free: 0.26
RfactorNum. reflection% reflection
Rfree0.284 4235 5.031 %
Rwork0.211 --
all-84172 -
obs-84172 -
Refinement stepCycle: LAST / Resolution: 2.14→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12360 0 462 1082 13904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONp_bond_d0.0150.0213030
X-RAY DIFFRACTIONp_angle_d0.0420.0417592
X-RAY DIFFRACTIONp_planar_d0.0450.053930
X-RAY DIFFRACTIONp_plane_restr0.0120.0210603
X-RAY DIFFRACTIONp_chiral_restr0.1410.151995
X-RAY DIFFRACTIONp_singtor_nbd0.2020.34899
X-RAY DIFFRACTIONp_multtor_nbd0.2540.37662
X-RAY DIFFRACTIONp_xyhbond_nbd0.1870.3572
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3040.385
X-RAY DIFFRACTIONp_planar_tor4.35771590
X-RAY DIFFRACTIONp_staggered_tor18.01152580
X-RAY DIFFRACTIONp_orthonormal_tor14.7920120
X-RAY DIFFRACTIONp_mcbond_it2.5827390
X-RAY DIFFRACTIONp_mcangle_it3.87438817
X-RAY DIFFRACTIONp_scbond_it2.90225640
X-RAY DIFFRACTIONp_scangle_it4.1438775
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.14-2.24250.3134850.235989611333
2.243-2.35540.314930.222944210230
2.355-2.48020.3244820.21585739338
2.48-2.6190.3124120.20676948350
2.619-2.77420.2893580.19969537488
2.774-2.9490.2913340.19761856633
2.949-3.14720.2952960.19954745854
3.147-3.37410.2712660.248415153
3.374-3.63620.2712380.19741764431
3.636-3.94250.2362020.19635873798
3.943-4.30510.2441550.19630543219
4.305-4.74120.2381160.18925702687
4.741-5.27560.2751010.19320882190
5.276-5.94580.323790.22716911770
5.946-6.81090.348760.2712811357
6.811-7.97080.274480.2769721021
7.971-9.60680.28390.299681733
9.607-12.08770.266320.298431485
12.088-16.29610.303150.32273300
16.296-250.28780.41275145
Refinement
*PLUS
Highest resolution: 2.14 Å / Lowest resolution: 25 Å / Rfactor obs: 0.2096 / Rfactor Rfree: 0.2879 / Rfactor Rwork: 0.2096
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.045

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