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- PDB-3ny6: Catalytic fragment of cholix toxin from vibrio cholerae in comple... -

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Basic information

Entry
Database: PDB / ID: 3ny6
TitleCatalytic fragment of cholix toxin from vibrio cholerae in complex with inhibitor V30
ComponentsCholix toxin
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ALPHA-BETA COMPLEX / ADP-ribosyl Transferase / NAD+ binding / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity
Similarity search - Function
Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Concanavalin A-like lectin/glucanase domain superfamily ...Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chem-V30 / Cholix toxin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsMerrill, A.R. / Jorgensen, R.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2011
Title: Newly discovered and characterized antivirulence compounds inhibit bacterial mono-ADP-ribosyltransferase toxins.
Authors: Turgeon, Z. / Jorgensen, R. / Visschedyk, D. / Edwards, P.R. / Legree, S. / McGregor, C. / Fieldhouse, R.J. / Mangroo, D. / Schapira, M. / Merrill, A.R.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 6, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholix toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9275
Polymers23,3351
Non-polymers5934
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.489, 64.973, 86.603
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cholix toxin


Mass: 23334.842 Da / Num. of mol.: 1 / Fragment: C-terminal catalytic domain, residues 459-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: TP / Gene: chxa, toxA / Plasmid: pET28A+ / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q5EK40, NAD+-diphthamide ADP-ribosyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-V30 / 2-[(5,6-dimethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-(2-hydroxyethyl)acetamide


Mass: 313.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N3O3S2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% PEG-8000, 0.02 M KH2PO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2010
Details: Multilayer mirror, curved to focus in the vertical (R = 400 m)
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03796 Å / Relative weight: 1
ReflectionResolution: 1.68→30 Å / Num. all: 23603 / Num. obs: 23558 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 23.237 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.59
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.68-1.725.40.5233.790951695169599.9
1.72-1.775.70.4064.4951016831683100
1.77-1.825.70.3235.6911616011601100
1.82-1.885.70.2437.289911586158699.9
1.88-1.945.70.1839.186341525152599.8
1.94-2.015.70.13911.8850114981498100
2.01-2.085.70.1213.4815714411441100
2.08-2.175.70.09716.278781383138399.9
2.17-2.275.70.08418.775141324132499.9
2.27-2.385.60.06921.271801276127699.9
2.38-2.55.70.06323.168771210121099.8
2.5-2.665.70.05725.565151151115199.7
2.66-2.845.60.04928.861961101110199.9
2.84-3.075.60.04132.3565110101010100
3.07-3.365.60.03538530394394399.6
3.36-3.765.50.03243.3471785885899.7
3.76-4.345.40.02947.8422878278299.6
4.34-5.315.40.02648.4346064264299.2
5.31-7.515.20.02746.62798537537100
7.51-304.60.02246144032731295.4

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Phasing

Phasing MRRfactor: 39.4 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.31 Å
Translation2.5 Å29.31 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q6M

2q6m


Resolution: 1.68→29.31 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.87 / SU B: 3.738 / SU ML: 0.059 / SU R Cruickshank DPI: 0.108 / SU Rfree: 0.107 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1178 5 %RANDOM
Rwork0.174 ---
obs0.176 23557 100 %-
all-23557 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 43.25 Å2 / Biso mean: 17.342 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.68→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 37 266 1850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211628
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9562216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33223.54479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4415247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8691513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211264
X-RAY DIFFRACTIONr_mcbond_it0.6221.5985
X-RAY DIFFRACTIONr_mcangle_it1.06121588
X-RAY DIFFRACTIONr_scbond_it1.8693643
X-RAY DIFFRACTIONr_scangle_it3.0324.5627
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 84 -
Rwork0.259 1608 -
all-1692 -
obs-1608 100 %
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)
10.0092-0.30950.077420.70080.06694.36160.05790.02220.0284-0.6813-0.1913-0.81860.4060.35220.13350.14770.03310.04650.14050.03850.18940.76212.399-19.538
24.689-0.79680.17946.1574-2.91365.20850.1050.29420.1016-0.4753-0.0332-0.19330.0260.0632-0.07180.05550.00180.04240.0708-0.00510.05691.828-2.295-21.353
31.9625-0.00840.01512.5693-0.48961.19840.0041-0.15870.18160.14380.01370.0179-0.1113-0.0153-0.01780.0416-0.0040.01310.0498-0.00190.0335-10.974.915-10.046
411.0922-4.65873.643131.172613.389714.5907-0.1416-0.417-0.17752.0968-0.30210.8390.3265-0.22940.44370.25180.01860.05960.2033-0.00870.0717-16.61225.77-9.45
50.2296-1.03740.15664.91-0.68890.4313-0.0197-0.00390.05390.013-0.0076-0.093-0.1455-0.09080.02730.07820.0107-0.02190.0757-0.00440.1156-11.40219.718-16.229
65.38690.4357-0.91193.2825-1.00460.5366-0.0169-0.0934-0.33140.0043-0.0462-0.17180.1011-0.00710.06310.0943-0.0111-0.0250.05520.0130.0339-11.908-10.837-7.085
73.9737-1.24613.59543.0569-1.84957.60570.0278-0.30560.06760.20660.06230.3083-0.146-0.2153-0.09010.0575-0.02320.03550.08440.00430.0499-24.797-7.4320.947
82.5620.7326-0.56851.12620.02350.19470.0561-0.20310.04110.1179-0.0559-0.0005-0.02460.0349-0.00010.0522-0.0002-0.00740.0455-0.0110.008-14.119-2.299-5.876
91.9933-1.8235-0.121611.9084.90854.3029-0.01090.19270.1527-0.5497-0.00650.3582-0.2343-0.12130.01740.0865-0.0227-0.00850.08550.04510.0664-13.9589.965-24.38
106.01744.8232-6.75557.4963-7.094711.222-0.29370.3309-0.225-0.40330.22610.10920.5035-0.42560.06760.0613-0.0004-0.02450.0537-0.01680.0457-12.896-9.181-17.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A425 - 435
2X-RAY DIFFRACTION2A436 - 452
3X-RAY DIFFRACTION3A453 - 507
4X-RAY DIFFRACTION4A508 - 513
5X-RAY DIFFRACTION5A514 - 531
6X-RAY DIFFRACTION6A532 - 545
7X-RAY DIFFRACTION7A546 - 562
8X-RAY DIFFRACTION8A563 - 598
9X-RAY DIFFRACTION9A599 - 616
10X-RAY DIFFRACTION10A617 - 628

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