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- PDB-1fd7: HEAT-LABILE ENTEROTOXIN B-PENTAMER WITH BOUND LIGAND BMSC001 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1fd7
TitleHEAT-LABILE ENTEROTOXIN B-PENTAMER WITH BOUND LIGAND BMSC001
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
N-BENZYL-3-(ALPHA-D-GALACTOS-1-YL)-BENZAMIDE / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsFan, E. / Merritt, E.A. / Pickens, J. / Ahn, M. / Hol, W.G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Exploration of the GM1 receptor-binding site of heat-labile enterotoxin and cholera toxin by phenyl-ring-containing galactose derivatives.
Authors: Fan, E. / Merritt, E.A. / Zhang, Z. / Pickens, J.C. / Roach, C. / Ahn, M. / Hol, W.G.
History
DepositionJul 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,96920
Polymers118,07510
Non-polymers3,89410
Water15,421856
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)60,98510
Polymers59,0385
Non-polymers1,9475
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16690 Å2
ΔGint-38 kcal/mol
Surface area20580 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)60,98510
Polymers59,0385
Non-polymers1,9475
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16730 Å2
ΔGint-33 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.761, 157.538, 63.145
Angle α, β, γ (deg.)90.00, 116.53, 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.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PROFIT / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P32890
#2: Chemical
ChemComp-AI1 / N-BENZYL-3-(ALPHA-D-GALACTOS-1-YL)-BENZAMIDE / N-BENZYL-3-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-BENZAMIDE / BMSC001 / 3-BENZYLAMINOCARBONYLPHENYL-ALPHA-D-GALACTOSIDE / BAPG


Mass: 389.399 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C20H23NO7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 856 / 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: 46.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 5000, NaCl, Tris/HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 mg/mlprotein1drop
250 mMTris-HCl1drop
32 mMBAPG1drop
450 mM1reservoirNaCl
5100 mMTris-HCl1reservoir
630 %(w/v)PEG50001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Apr 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 79747 / Num. obs: 79747 / % possible obs: 81.4 % / Redundancy: 2 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.132 / Num. unique all: 6180 / % possible all: 75.7
Reflection
*PLUS
Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 76 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
REFMACrefinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.8→20 Å / SU B: 3.174 / SU ML: 0.1 / ESU R: 0.182 / ESU R Free: 0.162 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3960 -RANDOM
Rwork0.187 ---
all0.187 75687 --
obs-75687 100 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8240 0 297 856 9393
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_mcbond_it0.6441
X-RAY DIFFRACTIONp_mcangle_it1.0151.5
X-RAY DIFFRACTIONp_scbond_it1.9222
X-RAY DIFFRACTIONp_scangle_it2.6943
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor14.915
X-RAY DIFFRACTIONp_transverse_tor13.520
X-RAY DIFFRACTIONp_special_tor015
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.1320.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.2450.3
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.031

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