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- PDB-3ki2: Catalytic fragment of Cholix toxin from Vibrio Cholerae in comple... -

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Basic information

Entry
Database: PDB / ID: 3ki2
TitleCatalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-G
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-G9G / Cholix toxin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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)23,9243
Polymers23,3351
Non-polymers5892
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)40.160, 64.870, 78.410
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-G9G / 2-(4-methylpiperazin-1-yl)benzo[c][1,5]naphthyridin-6(5H)-one


Mass: 294.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOMPOUND G9G IS NAMED COMPOUND P3 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: 2.18 Å3/Da / Density % sol: 43.49 %
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: 1.28→40 Å / Num. obs: 52851 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 20.832 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.48
Reflection shellResolution: 1.28→1.41 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 6 / Num. measured obs: 85197 / Num. unique all: 12948 / Num. unique obs: 12948 / % possible all: 97.2

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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: 1.28→18.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.892 / SU B: 1.628 / SU ML: 0.032 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2666 5 %RANDOM
Rwork0.181 ---
obs0.182 52847 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.02 Å2 / Biso mean: 19.505 Å2 / Biso min: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.28→18.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 44 270 1853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211677
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9712297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7475209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58824.16784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15615256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7391512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021325
X-RAY DIFFRACTIONr_nbd_refined0.1950.2742
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2199
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.216
X-RAY DIFFRACTIONr_mcbond_it1.4931.51032
X-RAY DIFFRACTIONr_mcangle_it2.18621619
X-RAY DIFFRACTIONr_scbond_it2.8183828
X-RAY DIFFRACTIONr_scangle_it3.7144.5671
X-RAY DIFFRACTIONr_rigid_bond_restr1.64731860
X-RAY DIFFRACTIONr_sphericity_free6.3893276
X-RAY DIFFRACTIONr_sphericity_bonded5.69931627
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 192 -
Rwork0.238 3382 -
all-3574 -
obs--91.5 %

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