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Basic information

Entry
Database: PDB / ID: 3efx
TitleNovel binding site identified in a hybrid between cholera toxin and heat-labile enterotoxin, 1.9A crystal structure reveals the details
ComponentsCholera enterotoxin subunit B, Heat-labile enterotoxin B chain
KeywordsTOXIN / PROTEIN-CARBOHYDRATE COMPLEX / CHOLERA TOXIN / HEAT-LABILE ENTEROTOXIN / BLOOD GROUP ANTIGEN
Function / homology
Function and homology information


toxin activity / 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
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsHolmner, A. / Lebens, M. / Teneberg, S. / Angstrom, J. / Okvist, M. / Krengel, U.
Citation
Journal: Structure / Year: 2004
Title: Novel binding site identified in a hybrid between cholera toxin and heat-labile enterotoxin: 1.9 A crystal structure reveals the details
Authors: Holmner, A. / Lebens, M. / Teneberg, S. / Angstrom, J. / Okvist, M. / Krengel, U.
#1: Journal: Structure / Year: 2007
Title: Novel binding site identified in a hybrid between cholera toxin and heat-labile enterotoxin: 1.9 A crystal structure reveals the details
Authors: Holmner, A. / Lebens, M. / Teneberg, S. / Angstrom, J. / Okvist, M. / Krengel, U.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: PDBJ
SupersessionSep 23, 2008ID: 2NZG
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 24, 2015Group: Source and taxonomy
Revision 1.3Sep 2, 2015Group: Source and taxonomy
Revision 1.4Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity_src_gen / struct_conn / struct_ref
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site ..._chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_seq_one_letter_code
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Apr 10, 2024Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
E: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
F: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
G: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
H: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
I: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
J: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
K: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
L: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
M: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,44020
Polymers116,06210
Non-polymers8,37810
Water15,997888
1
D: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
E: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
F: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
G: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
H: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,22010
Polymers58,0315
Non-polymers4,1895
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14130 Å2
ΔGint-2 kcal/mol
Surface area20430 Å2
MethodPISA
2
I: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
J: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
K: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
L: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
M: Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,22010
Polymers58,0315
Non-polymers4,1895
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-9 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.200, 70.100, 137.400
Angle α, β, γ (deg.)90.00, 92.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain


Mass: 11606.234 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: JS1569 / Plasmid: PML-LCTBK / Production host: VIBRIO CHOLERAE (bacteria) / References: UniProt: P0CK94*PLUS
#2: Polysaccharide
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]beta-D-glucopyranose


Type: oligosaccharide / Mass: 837.771 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-4[LFucpa1-3]DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a1221m-1a_1-5][a2112h-1b_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-2-4/a3-b1_a4-c1_c2-d1_c3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBLOOD GROUP A TYPE-2 PENTASACCHARIDE GALNACA3(FUCA2)GALB4(FUCA3)GLCB
Sequence detailsSEQUENCE IS A HYBRID BETWEEN THE B-SUBUNITS FROM CHOLERA TOXIN AND THE HEAT-LABILE ENTEROTOXIN FROM ...SEQUENCE IS A HYBRID BETWEEN THE B-SUBUNITS FROM CHOLERA TOXIN AND THE HEAT-LABILE ENTEROTOXIN FROM ESCHERICHIA COLI, DIFFERING FROM THE CLASSICAL CHOLERA TOXIN SEQUENCE AT POSITIONS 1, 7, 10, 18, 20, 25, 94 AND 95 (SEQUENCE FOR THE HYBRID IS NOT DEPOSITED IN ANY SEQUENCE DATABASE)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23-24% PEG 3350, 0.25-0.3M CALCIUM CHLORIDE, 20% GLYCEROL, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONMAX II I71110.97
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetector
MAR CCD 165 mm1CCD
MAR scanner 345 mm plate2IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.54181
ReflectionResolution: 1.94→19.44 Å / Num. all: 77618 / Num. obs: 74812 / % possible obs: 96 % / Observed criterion σ(F): -3.2 / Observed criterion σ(I): -3.2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.6
Reflection shellResolution: 1.94→1.99 Å / % possible all: 92.94

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EEI

1eei


Resolution: 1.94→19.44 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23179 3773 5 %RANDOM
Rwork0.181 ---
all0.18359 71039 --
obs0.18359 71039 --
Displacement parametersBiso mean: 23.064 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-2.11 Å2
2---0.24 Å20 Å2
3---0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.165 Å0.18 Å
Luzzati sigma a-0.111 Å
Refinement stepCycle: LAST / Resolution: 1.94→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7402 0 570 888 8860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.012
X-RAY DIFFRACTIONr_angle_refined_deg1.387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.663
X-RAY DIFFRACTIONr_chiral_restr0.086
X-RAY DIFFRACTIONr_gen_planes_refined0.005
X-RAY DIFFRACTIONr_nbd_refined0.209
X-RAY DIFFRACTIONr_nbtor_refined0.307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.155
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.191
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.156
X-RAY DIFFRACTIONr_mcbond_it0.805
X-RAY DIFFRACTIONr_mcangle_it1.244
X-RAY DIFFRACTIONr_scbond_it1.811
X-RAY DIFFRACTIONr_scangle_it2.772
LS refinement shellResolution: 1.94→1.99 Å
RfactorNum. reflection% reflection
Rfree0.285 263 -
Rwork0.205 --
obs-5044 92.94 %

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