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Basic information

Entry
Database: PDB / ID: 2xrq
TitleCrystal structures exploring the origins of the broader specificity of escherichia coli heat-labile enterotoxin compared to cholera toxin
ComponentsHEAT-LABILE ENTEROTOXIN B CHAIN
KeywordsTOXIN / HOST-PATHOGEN INTERACTIONS / MOLECULAR RECOGNITION / PROTEIN-CARBOHYDRATE INTERACTION
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
Heat-labile enterotoxin B chain / Enterotoxin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHolmner, A. / Mackenzie, A. / Okvist, M. / Jansson, L. / Lebens, M. / Teneberg, S. / Krengel, U.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structures Exploring the Origins of the Broader Specificity of Escherichia Coli Heat-Labile Enterotoxin Compared to Cholera Toxin
Authors: Holmner, A. / Mackenzie, A. / Okvist, M. / Jansson, L. / Lebens, M. / Teneberg, S. / Krengel, U.
History
DepositionSep 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references / Version format compliance
Revision 1.2Apr 1, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,03210
Polymers59,0385
Non-polymers4,9945
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23050 Å2
ΔGint28.5 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.009, 96.099, 66.289
Angle α, β, γ (deg.)90.00, 97.22, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21E
31F
41G
51H
12D
22E
32F
42G
52H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111D1 - 5
2111E1 - 5
3111F1 - 5
4111G1 - 5
5111H1 - 5
1213D6
2213E6
3213F6
4213G6
5213H6
1311D7 - 9
2311E7 - 9
3311F7 - 9
4311G7 - 9
5311H7 - 9
1413D10
2413E10
3413F10
4413G10
5413H10
1511D11 - 12
2511E11 - 12
3511F11 - 12
4511G11 - 12
5511H11 - 12
1616D13
2616E13
3616F13
4616G13
5616H13
1711D14 - 22
2711E14 - 22
3711F14 - 22
4711G14 - 22
5711H14 - 22
1813D23
2813E23
3813F23
4813G23
5813H23
1911D24 - 33
2911E24 - 33
3911F24 - 33
4911G24 - 33
5911H24 - 33
11016D34
21016E34
31016F34
41016G34
51016H34
11111D35 - 42
21111E35 - 42
31111F35 - 42
41111G35 - 42
51111H35 - 42
11213D43 - 46
21213E43 - 46
31213F43 - 46
41213G43 - 46
51213H43 - 46
11311D47 - 103
21311E47 - 103
31311F47 - 103
41311G47 - 103
51311H47 - 103
1126D104 - 108
2126E104 - 108
3126F104 - 108
4126G104 - 108
5126H104 - 108

NCS ensembles :
ID
1
2

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Components

#1: Protein
HEAT-LABILE ENTEROTOXIN B CHAIN / LTH-B


Mass: 11807.539 Da / Num. of mol.: 5 / Fragment: RESIDUES 22-124
Source method: isolated from a genetically manipulated source
Details: PORCINE ENTEROTOXIN PLT B-SUBUNIT CONTAINING GM1 PENTASACCHARIDE(GAL-BETA3-GALNAC-BETA4 (NEUAC ALPHA3)-GAL-BETA4 -GLC
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PMLPLTBTAC / Production host: VIBRIO CHOLERAE (bacteria) / Strain (production host): JS1569 / References: UniProt: Q0PRR7, UniProt: P32890*PLUS
#2: Polysaccharide
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2/a4-b1_b3-c2_b4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMATURE PROTEIN AFTER CLEAVAGE OF SIGNAL PEPTIDE

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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: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 7.5
Details: 17-19% PEG3350, 150-210 MM NASO4, 7% GLYCEROL, 100 MM BIS-TRIS PROPANE, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 26414 / % possible obs: 96.9 % / Observed criterion σ(I): 1.5 / Redundancy: 2.1 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EFI

1efi


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / SU B: 19.031 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23517 1319 5 %RANDOM
Rwork0.21173 ---
obs0.21296 25090 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.668 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å2-0.67 Å2
2---0.85 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 340 116 4576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224540
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3952.0526165
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7625.429175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26215840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6171520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213060
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2281.52575
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.39824230
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.96831965
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.384.51940
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11D782tight positional0.040.05
12E782tight positional0.040.05
13F782tight positional0.040.05
14G782tight positional0.040.05
15H782tight positional0.040.05
11D42loose positional0.055
12E42loose positional0.045
13F42loose positional0.045
14G42loose positional0.055
15H42loose positional0.045
21D68loose positional0.365
22E68loose positional0.35
23F68loose positional0.215
24G68loose positional0.25
25H68loose positional0.355
11D782tight thermal0.090.5
12E782tight thermal0.10.5
13F782tight thermal0.090.5
14G782tight thermal0.080.5
15H782tight thermal0.090.5
11D42loose thermal0.0810
12E42loose thermal0.0910
13F42loose thermal0.0810
14G42loose thermal0.0910
15H42loose thermal0.0710
21D68loose thermal1.9310
22E68loose thermal2.5510
23F68loose thermal1.3810
24G68loose thermal1.3210
25H68loose thermal1.8410
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 88 -
Rwork0.37 1873 -
obs--95.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0338-1.53430.1574.3966-0.46264.0926-0.26570.30851.03180.38630.0368-0.6452-0.7884-0.04170.22890.4278-0.0232-0.09940.12080.09150.329214.240919.015616.0487
24.1566-1.74632.35554.5946-0.44453.8542-0.04491.84540.3342-0.2508-0.5546-0.7566-0.35640.52550.59950.1325-0.02320.14140.84840.16480.230317.50686.2529-2.5745
33.82640.16161.57745.2321-1.34543.60570.28471.212-1.1965-0.0672-0.1146-0.61390.44330.5234-0.17010.12050.09650.08030.5017-0.38760.532420.4205-15.50394.1356
43.2784-0.87150.40682.8868-0.16434.50080.0473-0.3217-0.930.64460.0599-0.21120.2549-0.078-0.10720.3358-0.0062-0.04360.12040.05870.453918.8667-16.08426.9988
53.8855-1.19280.26864.2980.03623.3777-0.3787-0.77810.24830.89130.2307-0.3595-0.4187-0.1120.1480.57140.0709-0.12230.2434-0.03020.126915.32775.37434.3789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 103
2X-RAY DIFFRACTION1D1104 - 1108
3X-RAY DIFFRACTION2E1 - 103
4X-RAY DIFFRACTION2E1104 - 1108
5X-RAY DIFFRACTION3F1 - 103
6X-RAY DIFFRACTION3F1104 - 1108
7X-RAY DIFFRACTION4G1 - 103
8X-RAY DIFFRACTION4G1104 - 1108
9X-RAY DIFFRACTION5H1 - 103
10X-RAY DIFFRACTION5H1104 - 1108

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