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- PDB-1s5f: Cholera holotoxin, Crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 1s5f
TitleCholera holotoxin, Crystal form 2
Components
  • Cholera enterotoxin, A chain
  • cholera toxin B protein (CTB)
KeywordsTRANSFERASE / TOXIN / cholera toxin / heat-labile enterotoxin / ADP ribose transferases / AB5 toxins
Function / homology
Function and homology information


host cell surface binding / galactose binding / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / toxin activity / periplasmic space / lipid binding ...host cell surface binding / galactose binding / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / toxin activity / periplasmic space / lipid binding / host cell plasma membrane / extracellular space / extracellular region / membrane
Similarity search - Function
Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex ...Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Cholera enterotoxin subunit A / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsO'Neal, C.J. / Amaya, E.I. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal structures of an intrinsically active cholera toxin mutant yield insight into the toxin activation mechanism
Authors: O'Neal, C.J. / Amaya, E.I. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.
History
DepositionJan 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholera enterotoxin, A chain
D: cholera toxin B protein (CTB)
E: cholera toxin B protein (CTB)
F: cholera toxin B protein (CTB)
G: cholera toxin B protein (CTB)
H: cholera toxin B protein (CTB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,26912
Polymers85,3456
Non-polymers9246
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Cholera enterotoxin, A chain
hetero molecules

D: cholera toxin B protein (CTB)
E: cholera toxin B protein (CTB)
F: cholera toxin B protein (CTB)
G: cholera toxin B protein (CTB)
H: cholera toxin B protein (CTB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,26912
Polymers85,3456
Non-polymers9246
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
identity operation1_555x,y,z1
Buried area14200 Å2
ΔGint-49 kcal/mol
Surface area30580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.157, 110.970, 123.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cholera enterotoxin, A chain / NAD(+)--diphthamide ADP- ribosyltransferase / Cholera enterotoxin A subunit


Mass: 27228.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CTXA, TOXA, VC1457 / Plasmid: pARCT5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P01555, NAD+-diphthamide ADP-ribosyltransferase
#2: Protein
cholera toxin B protein (CTB)


Mass: 11623.267 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CTXB, TOXB, VC1456 / Plasmid: pARCT5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01556
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.57 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: PEG 3350, lithium citrate, galactose, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.6→48.62 Å / Num. all: 24832 / Num. obs: 24832 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.133 / Net I/σ(I): 10.2
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2.75 / Num. unique all: 2478 / Rsym value: 0.546 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CTY30S Form 3 structure (PDB ID 1S5B)

1s5b


Resolution: 2.6→28.99 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.874 / SU B: 11.201 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.554 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26031 1263 5.1 %RANDOM
Rwork0.21335 ---
all0.21565 23550 --
obs0.21565 23550 94.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.277 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5660 0 61 59 5780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215844
X-RAY DIFFRACTIONr_bond_other_d0.0030.025063
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9387941
X-RAY DIFFRACTIONr_angle_other_deg0.88311751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365730
X-RAY DIFFRACTIONr_chiral_restr0.0670.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026536
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021133
X-RAY DIFFRACTIONr_nbd_refined0.170.31099
X-RAY DIFFRACTIONr_nbd_other0.1890.35794
X-RAY DIFFRACTIONr_nbtor_other0.0850.53294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.5163
X-RAY DIFFRACTIONr_metal_ion_refined0.30.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.57
LS refinement shellResolution: 2.6→2.664 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 98
Rwork0.302 1686

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