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- PDB-3ki6: Catalytic fragment of Cholix toxin from Vibrio Cholerae in comple... -

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Basic information

Entry
Database: PDB / ID: 3ki6
TitleCatalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-L
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 / 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
Chem-G9L / Cholix toxin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 1.2Nov 1, 2017Group: Refinement description / Category: software
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)23,6922
Polymers23,3351
Non-polymers3571
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.349, 64.870, 78.600
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-G9L / 8-fluoro-2-(3-piperidin-1-ylpropanoyl)-1,3,4,5-tetrahydrobenzo[c][1,6]naphthyridin-6(2H)-one


Mass: 357.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24FN3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOMPOUND G9L IS NAMED COMPOUND P6 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: 2.19 Å3/Da / Density % sol: 43.89 %
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: 1.54→50 Å / Num. obs: 31156 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.9
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2918 / % possible all: 95

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MacromolecularCrystallography Data Collection (MXDC) GUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q6M

2q6m


Resolution: 1.54→21.97 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.892 / SU B: 2.215 / SU ML: 0.044 / Isotropic thermal model: Isotropic with 10 TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1562 5 %RANDOM
Rwork0.174 ---
obs0.176 31099 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.12 Å2 / Biso mean: 16.878 Å2 / Biso min: 6.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.54→21.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 26 270 1835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211632
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9542230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4935204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.99523.79779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08815250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6441512
X-RAY DIFFRACTIONr_chiral_restr0.110.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021277
X-RAY DIFFRACTIONr_nbd_refined0.2050.2715
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21137
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2197
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.222
X-RAY DIFFRACTIONr_mcbond_it1.1171.51022
X-RAY DIFFRACTIONr_mcangle_it1.59621603
X-RAY DIFFRACTIONr_scbond_it2.4933725
X-RAY DIFFRACTIONr_scangle_it3.7834.5623
LS refinement shellResolution: 1.54→1.579 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 90 -
Rwork0.195 2015 -
all-2105 -
obs--93.18 %
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)
14.26535.38753.0158.20613.49392.2017-0.21540.0924-0.0862-0.07850.1486-0.10090.00140.17670.0667-0.05480.00080.0166-0.02310.01880.111239.38553.60114.381
21.98440.41130.90456.7572-4.61284.4618-0.0452-0.10420.0440.0899-0.0033-0.4548-0.16150.06880.0485-0.064-0.0042-0.00640.014-0.00330.053539.1267.06817.455
31.2043-0.0206-0.05142.0683-0.50760.70680.03430.11050.0007-0.2075-0.02680.01860.09730.0979-0.00750.00630.00870.00680.00690.0065-0.005229.2661.7115.367
40.0525-0.18460.16121.528-0.18881.4514-0.0023-0.0401-0.0537-0.13550.00990.10580.0438-0.1802-0.0077-0.0028-0.0084-0.00890.01670.01060.026319.22460.139.988
512.52284.780210.37784.93623.73510.9358-0.69880.0784-0.4109-1.05740.5075-0.3012-0.8749-0.10680.19140.1405-0.05520.0211-0.0309-0.0183-0.069520.95537.96110.376
60.67820.1475-0.02621.471-0.31810.7454-0.01770.010.032-0.11310.0084-0.1008-0.02470.04260.0093-0.0026-0.00920.0103-0.00710.0089-0.00626.12468.3278.119
72.17261.4091-2.58664.5799-2.11169.3028-0.20210.05430.0635-0.33430.18320.40080.0899-0.45560.0189-0.04730.0171-0.0580.00560.02870.04227.73571.982.251
80.67620.02820.1431.2442-0.25290.90050.04160.0207-0.011-0.2153-0.00510.08960.00470.0021-0.03650.00530.0073-0.0051-0.01060.0075-0.013220.69167.7714.059
91.45333.57961.450716.94558.12635.71380.0559-0.15060.03540.5458-0.22740.36180.3901-0.14870.1715-0.0112-0.00630.0091-0.01330.0203-0.009323.08854.02222.025
103.2234-2.44583.26923.3075-2.98434.5816-0.1456-0.13250.08590.12890.1448-0.0097-0.3493-0.00030.0007-0.0021-0.00050.0051-0.013-0.00880.019724.93273.53815.978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A423 - 436
2X-RAY DIFFRACTION2A437 - 450
3X-RAY DIFFRACTION3A451 - 487
4X-RAY DIFFRACTION4A488 - 507
5X-RAY DIFFRACTION5A508 - 522
6X-RAY DIFFRACTION6A523 - 544
7X-RAY DIFFRACTION7A545 - 557
8X-RAY DIFFRACTION8A558 - 601
9X-RAY DIFFRACTION9A602 - 615
10X-RAY DIFFRACTION10A616 - 628

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