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- PDB-1lt6: HEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH METANITROPHENYL... -

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Basic information

Entry
Database: PDB / ID: 1lt6
TitleHEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH METANITROPHENYLGALACTOSIDE
ComponentsHEAT-LABILE ENTEROTOXINHeat-labile enterotoxin family
KeywordsENTEROTOXIN
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
3-nitrophenyl alpha-D-galactopyranoside / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
Citation
Journal: Structure / Year: 1997
Title: Structural foundation for the design of receptor antagonists targeting Escherichia coli heat-labile enterotoxin.
Authors: Merritt, E.A. / Sarfaty, S. / Feil, I.K. / Hol, W.G.
#1: Journal: Mol.Microbiol. / Year: 1994
Title: Galactose-Binding Site in Escherichia Coli Heat-Labile Enterotoxin (Lt) and Cholera Toxin (Ct)
Authors: Merritt, E.A. / Sixma, T.K. / Kalk, K.H. / Van Zanten, B.A. / Hol, W.G.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Structure of Escherichia Coli Heat-Labile Enterotoxin, a Close Relative of Cholera Toxin
Authors: Sixma, T.K. / Kalk, K.H. / Van Zanten, B.A. / Dauter, Z. / Kingma, J. / Witholt, B. / Hol, W.G.
History
DepositionOct 1, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: HEAT-LABILE ENTEROTOXIN
E: HEAT-LABILE ENTEROTOXIN
F: HEAT-LABILE ENTEROTOXIN
G: HEAT-LABILE ENTEROTOXIN
H: HEAT-LABILE ENTEROTOXIN
L: HEAT-LABILE ENTEROTOXIN
M: HEAT-LABILE ENTEROTOXIN
N: HEAT-LABILE ENTEROTOXIN
O: HEAT-LABILE ENTEROTOXIN
P: HEAT-LABILE ENTEROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,08820
Polymers118,07510
Non-polymers3,01210
Water4,540252
1
D: HEAT-LABILE ENTEROTOXIN
E: HEAT-LABILE ENTEROTOXIN
F: HEAT-LABILE ENTEROTOXIN
G: HEAT-LABILE ENTEROTOXIN
H: HEAT-LABILE ENTEROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,54410
Polymers59,0385
Non-polymers1,5065
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: HEAT-LABILE ENTEROTOXIN
M: HEAT-LABILE ENTEROTOXIN
N: HEAT-LABILE ENTEROTOXIN
O: HEAT-LABILE ENTEROTOXIN
P: HEAT-LABILE ENTEROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,54410
Polymers59,0385
Non-polymers1,5065
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.670, 95.360, 85.650
Angle α, β, γ (deg.)90.00, 100.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HEAT-LABILE ENTEROTOXIN / Heat-labile enterotoxin family / LT-I


Mass: 11807.539 Da / Num. of mol.: 10 / Fragment: B-PENTAMER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINEPig / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P32890
#2: Sugar
ChemComp-GAA / 3-nitrophenyl alpha-D-galactopyranoside / METANITROPHENYL-ALPHA-D-GALACTOSIDE / 3-nitrophenyl alpha-D-galactoside / 3-nitrophenyl D-galactoside / 3-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C12H15NO8
IdentifierTypeProgram
metanitrophenyl-a-D-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: batch method / Details: three-layered solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
2100 mMTris-HCl11
3200 mM11NaCl
40.5 mMEDTA11
50.1 mMazide11
6200 mMthiodigalactoside12
7100 mMTris-HCl12
842 %PEG600013
9100 mMTris-HCl13
1protein11
1050 mM13NaCl

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1996 / Details: DOUBLY-FOCUSED MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 51781 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Redundancy: 2.23 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.298 / % possible all: 71.8
Reflection shell
*PLUS
% possible obs: 72 %

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Processing

Software
NameVersionClassification
XENGENdata collection
MACROdata reduction
AMoREphasing
X-PLOR3.1refinement
XENGENdata reduction
MACROdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTA

1lta


Resolution: 2.2→25 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BABINET BULK SOLVENT MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.273 -7 %RANDOM
Rwork0.182 ---
obs0.182 46246 82.8 %-
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--5.742 Å20 Å21.669 Å2
2--1.919 Å20 Å2
3---3.822 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8240 0 210 252 8702
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.53
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.12
X-RAY DIFFRACTIONx_mcangle_it6.24
X-RAY DIFFRACTIONx_scbond_it4.12
X-RAY DIFFRACTIONx_scangle_it6.24
LS refinement shellResolution: 2.2→2.23 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.379 73
Rwork0.284 1093
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM1.CHOLOCALLY MODIFIED TOPH1.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.53

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