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- PDB-3ki7: Catalytic fragment of Cholix toxin from Vibrio Cholerae in comple... -

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Basic information

Entry
Database: PDB / ID: 3ki7
TitleCatalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-I
ComponentsCholix toxinPseudomonas exotoxin
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-G9I / Cholix toxin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 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)23,7092
Polymers23,3351
Non-polymers3741
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.467, 64.898, 91.756
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 / Pseudomonas exotoxin


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-G9I / 2-{2-[4-(pyrrolidin-1-ylmethyl)phenyl]ethyl}-5,6-dihydroimidazo[4,5,1-jk][1,4]benzodiazepin-7(4H)-one / 1-[2-(4-Pyrrolidin-1-ylmethyl-phenyl)-ethyl]-8,9-dihydro-7H-2,7,9a-triaza-benzo[cd]azulen-6-one


Mass: 374.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOMPOUND G9I IS NAMED COMPOUND P5 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: 2.25 Å3/Da / Density % sol: 45.34 %
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: 1.32→50 Å / Num. obs: 46297 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.121 / Χ2: 1.063 / Net I/σ(I): 5.8
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 5.6 / Num. unique all: 4380 / Χ2: 0.809 / % possible all: 87.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.41 Å18.85 Å
Translation1.41 Å18.85 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MacromolecularCrystallography Data Collection (MXDC) GUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q6M

2q6m


Resolution: 1.32→18.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.204 / SU ML: 0.024 / Isotropic thermal model: Isotropic with 10 TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 2338 5.1 %RANDOM
Rwork0.15 ---
obs0.152 46202 92.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.887 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.32→18.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 28 395 1977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221628
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9642221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80723.76677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15815250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2641512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021268
X-RAY DIFFRACTIONr_nbd_refined0.20.2741
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.237
X-RAY DIFFRACTIONr_mcbond_it1.0481.51016
X-RAY DIFFRACTIONr_mcangle_it1.54121599
X-RAY DIFFRACTIONr_scbond_it2.193711
X-RAY DIFFRACTIONr_scangle_it2.9194.5621
X-RAY DIFFRACTIONr_rigid_bond_restr1.10931727
X-RAY DIFFRACTIONr_sphericity_free4.2823395
X-RAY DIFFRACTIONr_sphericity_bonded2.53231587
LS refinement shellResolution: 1.32→1.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 192 -
Rwork0.134 3360 -
all-3552 -
obs--98.2 %

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