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- PDB-3ki1: Catalytic fragment of Cholix toxin from Vibrio Cholerae in comple... -

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Basic information

Entry
Database: PDB / ID: 3ki1
TitleCatalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-F
ComponentsCholix toxin
KeywordsTransferase / toxin / ADP-ribosyl transferase / alpha-beta complex / diphthamide
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / symbiont-mediated killing of host cell / nucleotidyltransferase activity / symbiont-mediated activation of host apoptosis / 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
Chem-G9F / Cholix toxin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsJorgensen, R. / Edwards, P.R. / Merrill, A.R.
CitationJournal: To be Published
Title: Structure function analysis of soluble inhibitors of cholix toxin from Vibrio cholerae
Authors: Jorgensen, R. / Edwards, P.R. / Merrill, A.R.
History
DepositionOct 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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)24,0643
Polymers23,3351
Non-polymers7292
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.120, 65.790, 78.080
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: 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: pET28+ / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q5EK40, NAD+-diphthamide ADP-ribosyltransferase
#2: Chemical ChemComp-G9F / 2-{4-[3-(dimethylamino)propoxy]phenyl}-5,6-dihydroimidazo[4,5,1-jk][1,4]benzodiazepin-7(4H)-one / 1-[4-(3-Dimethylamino-propoxy)-phenyl]-8,9-dihydro-7H-2,7,9a-triaza-benzo[cd]azulen-6


Mass: 364.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOMPOUND G9F IS NAMED COMPOUND P2 IN THE PRIMARY CITATION

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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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% PEG-8000, 0.02 M KH2PO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2008
RadiationMonochromator: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.43→40 Å / Num. obs: 37801 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.87
Reflection shellResolution: 1.43→1.57 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 3 / Num. measured obs: 56922 / Num. unique all: 8695 / Num. unique obs: 8695 / % possible all: 94.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MacromolecularCrystallography Data Collection (MXDC) GUIdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q6M

2q6m


Resolution: 1.43→19.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.89 / SU B: 2.193 / SU ML: 0.045 / Isotropic thermal model: Isotropic with 10 TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1881 5 %RANDOM
Rwork0.175 ---
obs0.177 37792 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.04 Å2 / Biso mean: 15.669 Å2 / Biso min: 4.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.43→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 54 260 1836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211638
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9772236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8875198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.10623.63677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41515243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3981512
X-RAY DIFFRACTIONr_chiral_restr0.1130.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021287
X-RAY DIFFRACTIONr_nbd_refined0.2020.2674
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.222
X-RAY DIFFRACTIONr_mcbond_it1.1261.51015
X-RAY DIFFRACTIONr_mcangle_it1.61521579
X-RAY DIFFRACTIONr_scbond_it2.6973750
X-RAY DIFFRACTIONr_scangle_it3.6754.5656
LS refinement shellResolution: 1.43→1.471 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 94 -
Rwork0.247 1922 -
all-2016 -
obs--72.83 %
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)
14.60196.0573.736113.75234.80383.0354-0.30890.1941-0.0748-0.0130.274-0.1030.05180.29970.0349-0.08960.01120.00280.04550.01680.130239.279754.21714.3481
20.60490.03520.16181.5586-0.26160.70950.00330.02240.0429-0.1331-0.0239-0.15090.01970.13730.0206-0.03870.00310.02460.06450.00790.03834.21565.184610.63
329.4637-8.3249-0.15716.7084-0.94247.02760.61321.036-1.2259-0.1519-0.29650.5085-0.1598-0.4317-0.31660.06620.0263-0.06910.0815-0.01740.054613.635864.1464-2.9438
40.2053-0.43860.15081.39130.47271.50150.0264-0.0646-0.02460.00080.01960.1050.0564-0.1391-0.046-0.0249-0.0078-0.00970.07050.01650.044520.322259.212212.5949
511.42725.57018.83395.44583.99247.7874-0.3358-0.0238-0.5252-0.85160.3597-0.4722-0.56210.0192-0.02390.0884-0.06110.04440.006-0.0046-0.030421.243837.571110.3472
60.58190.18570.06781.2477-0.49070.6092-0.01560.00060.0204-0.0460.0293-0.0799-0.03990.0327-0.0137-0.0093-0.00450.0160.04230.00590.016825.969369.23418.0944
74.5413.3816-4.17736.50871.20628.5125-0.350.02790.1102-0.03870.25050.49770.0741-0.54830.0995-0.09360.0345-0.04280.09040.06120.06266.996671.99813.8582
80.46380.0660.14311.1181-0.26830.85440.0461-0.00310.009-0.21090.01690.1097-0.0054-0.0078-0.0630.00240.0142-0.00980.04690.0140.008419.66369.53733.2553
91.41872.25371.45358.74685.26163.6932-0.0089-0.0441-0.0180.3379-0.04530.15680.2497-0.01690.05410.007-0.00130.00530.05430.02420.008523.090254.592421.7842
103.6747-2.05413.42121.9509-2.45844.2668-0.1289-0.15490.10170.1310.1339-0.037-0.3593-0.0581-0.0050.01230.00820.01190.0387-0.00820.025624.77874.521415.9804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A423 - 436
2X-RAY DIFFRACTION2A437 - 476
3X-RAY DIFFRACTION3A487 - 491
4X-RAY DIFFRACTION4A492 - 508
5X-RAY DIFFRACTION5A509 - 522
6X-RAY DIFFRACTION6A523 - 544
7X-RAY DIFFRACTION7A545 - 554
8X-RAY DIFFRACTION8A555 - 600
9X-RAY DIFFRACTION9A601 - 615
10X-RAY DIFFRACTION10A616 - 628

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