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- PDB-5lzh: Cholera toxin classical B-pentamer in complex with inhibitor PC262 -

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Basic information

Entry
Database: PDB / ID: 5lzh
TitleCholera toxin classical B-pentamer in complex with inhibitor PC262
Components(Cholera enterotoxin B ...) x 2
KeywordsTOXIN / cholera toxin B-pentamer / inhibitor
Function / homology
Function and homology information


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-7BN / DI(HYDROXYETHYL)ETHER / Cholera enterotoxin B-subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsHeggelund, J.E. / Martinsen, T. / Krengel, U.
CitationJournal: Sci Rep / Year: 2017
Title: Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics.
Authors: Heggelund, J.E. / Mackenzie, A. / Martinsen, T. / Benjamin Heim, J. / Cheshev, P. / Bernardi, A. / Krengel, U.
History
DepositionSep 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 2.0Feb 14, 2018Group: Atomic model / Derived calculations / Non-polymer description
Category: atom_site / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholera enterotoxin B subunit
B: Cholera enterotoxin B subunit
C: Cholera enterotoxin B subunit
D: Cholera enterotoxin B subunit
E: Cholera enterotoxin B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,78716
Polymers58,2125
Non-polymers3,57511
Water10,953608
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-65 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.736, 66.063, 76.389
Angle α, β, γ (deg.)90.00, 105.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Cholera enterotoxin B ... , 2 types, 5 molecules ABDCE

#1: Protein Cholera enterotoxin B subunit / Cholera enterotoxin B-subunit / Cholera enterotoxin subunit B / Cholera toxin B protein (CTB) / ...Cholera enterotoxin B-subunit / Cholera enterotoxin subunit B / Cholera toxin B protein (CTB) / Cholera toxin B subunit / Cholera toxin beta subunit / Cholera toxin subunit B / Cholerae toxin B subunit / CtxB


Mass: 11655.267 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: ctxB, EN12_07055, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003, ERS013207_03244
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57193
#2: Protein Cholera enterotoxin B subunit / Cholera enterotoxin B-subunit / Cholera enterotoxin subunit B / Cholera toxin B protein (CTB) / ...Cholera enterotoxin B-subunit / Cholera enterotoxin subunit B / Cholera toxin B protein (CTB) / Cholera toxin B subunit / Cholera toxin beta subunit / Cholera toxin subunit B / Cholerae toxin B subunit / CtxB


Mass: 11623.267 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: ctxB, EN12_07055, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003, ERS013207_03244
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57193

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Non-polymers , 6 types, 619 molecules

#3: Chemical
ChemComp-7BN / (2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[3-[2-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]ethylamino]-3-oxidanylidene-propyl]-1,2,3-triazol-1-yl]-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid


Mass: 621.592 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H39N5O14
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES/Imidazole pH 6.5, 8% PEG1000, 8% PEG 3350, 8% MPD, 0.03 M divalent cations

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.991872 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991872 Å / Relative weight: 1
ReflectionResolution: 1.13→49 Å / Num. obs: 135800 / % possible obs: 73.7 % / Redundancy: 2.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.87
Reflection shellResolution: 1.13→1.19 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 0.73 / CC1/2: 0.504 / % possible all: 13.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CHB

3chb


Resolution: 1.13→73.55 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.685 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22862 6823 5 %RANDOM
Rwork0.19734 ---
obs0.19895 128966 73.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.606 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20.01 Å2
2---0.9 Å20 Å2
3---1.88 Å2
Refinement stepCycle: 1 / Resolution: 1.13→73.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 241 608 4925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.024591
X-RAY DIFFRACTIONr_bond_other_d0.0060.024408
X-RAY DIFFRACTIONr_angle_refined_deg2.5011.9976256
X-RAY DIFFRACTIONr_angle_other_deg1.3733.01710221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7025558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.34225.103194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47615819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8821519
X-RAY DIFFRACTIONr_chiral_restr0.1550.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025023
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02992
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_it0.7910.9732133
X-RAY DIFFRACTIONr_mcbond_other0.780.972131
X-RAY DIFFRACTIONr_mcangle_it1.1431.4532679
X-RAY DIFFRACTIONr_mcangle_other1.1441.4542680
X-RAY DIFFRACTIONr_scbond_it1.2231.2012458
X-RAY DIFFRACTIONr_scbond_other1.2231.2012458
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8411.7573562
X-RAY DIFFRACTIONr_long_range_B_refined4.63414.1845396
X-RAY DIFFRACTIONr_long_range_B_other4.63314.185396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.125→1.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.581 46 -
Rwork0.512 825 -
obs--6.44 %
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)
10.6541-0.068-0.05760.6395-0.11330.4269-0.0440.06040.0691-0.03790.02380.1708-0.021-0.01630.02020.0095-0.007-0.01370.0420.01790.1369-18.86344.808911.7992
21.15440.2851-0.04030.6539-0.19020.4639-0.00490.00140.2555-0.00370.02480.1745-0.0153-0.0359-0.01990.0038-0.00050.01180.0064-0.0020.1452-3.531918.528419.2258
31.30680.09750.09220.94070.04670.11750.0236-0.17240.06120.0223-0.0156-0.026-0.0185-0.0036-0.0080.0103-0.01150.01480.0689-0.01240.036812.94956.53627.0954
41.5280.34730.27630.89790.29940.32970.0723-0.1236-0.36790.0734-0.0278-0.0772-0.0049-0.0009-0.04460.0192-0.0055-0.00390.04790.03890.13367.7589-14.530224.6783
51.48880.73090.28320.87690.14640.2474-0.00770.0797-0.08220.00710.00640.03370.0063-0.00290.00140.0032-0.00220.01590.0336-0.00160.0877-11.8147-15.706814.9395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2B1 - 103
3X-RAY DIFFRACTION3C1 - 103
4X-RAY DIFFRACTION4D1 - 103
5X-RAY DIFFRACTION5E1 - 103

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