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- PDB-3ki5: Catalytic fragment of Cholix toxin from Vibrio Cholerae in comple... -

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Basic information

Entry
Database: PDB / ID: 3ki5
TitleCatalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-M
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-G9M / Cholix toxin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)24,1463
Polymers23,3351
Non-polymers8112
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.284, 64.582, 77.836
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-G9M / N-(6-oxo-5,6-dihydrobenzo[c][1,5]naphthyridin-2-yl)-2-(4-pyrrolidin-1-ylpiperidin-1-yl)acetamide


Mass: 405.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOMPOUND G9M IS NAMED COMPOUND P7 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: 2.16 Å3/Da / Density % sol: 42.99 %
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: 1.55→30 Å / Num. obs: 28938 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.057 / Χ2: 0.976 / Net I/σ(I): 13.7
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2080 / Χ2: 0.79 / % possible all: 70.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MXData Collectiondata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q6M

2q6m


Resolution: 1.55→21.15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.842 / SU B: 3.325 / SU ML: 0.065 / Isotropic thermal model: Isotropic with 10 TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1456 5 %RANDOM
Rwork0.2 ---
obs0.202 28871 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.73 Å2 / Biso mean: 20.374 Å2 / Biso min: 9.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.55→21.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 60 280 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211680
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.9772298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5065204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7224.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02715248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8171511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021306
X-RAY DIFFRACTIONr_nbd_refined0.190.2736
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.221
X-RAY DIFFRACTIONr_mcbond_it0.6451.51052
X-RAY DIFFRACTIONr_mcangle_it0.99821638
X-RAY DIFFRACTIONr_scbond_it1.5853818
X-RAY DIFFRACTIONr_scangle_it2.2884.5658
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 75 -
Rwork0.275 1395 -
all-1470 -
obs--67.18 %
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)
110.69129.46496.14069.07384.97973.8271-0.40340.0432-0.2538-0.18090.1954-0.38520.04020.430.208-0.04350.04390.0150.03940.01490.185139.35653.01314.291
20.55820.12670.08281.9906-0.64410.89840.0102-0.04250.0959-0.1623-0.1083-0.16820.04520.20060.0981-0.0570.00910.03780.06960.01690.086834.42163.60511.414
329.0538-4.66623.07544.7459-0.55092.45710.15871.139-1.9636-0.4263-0.07060.77410.4614-0.1481-0.08810.1491-0.0576-0.06990.0414-0.04880.08417.47460.26-2.998
40.7241-0.1064-0.0111.58270.21520.7852-0.0218-0.0482-0.0138-0.03330.0740.18180.0648-0.1527-0.0523-0.0139-0.0015-0.00170.03190.00620.089320.3558.7711.832
511.51827.82477.74438.37765.470611.8874-0.6398-0.0442-0.6276-1.33130.5313-0.6931-0.7814-0.23080.10850.1644-0.050.1236-0.0387-0.00920.023921.22737.18710.143
60.50610.04240.07911.6577-0.05820.7659-0.06120.03230.0405-0.16820.05120.143-0.0408-0.00630.01-0.0229-0.0078-0.00430.02110.02280.079718.68769.8443.203
70.3670.2036-0.31831.6418-0.75411.40580.03070.01170.0053-0.1540.00510.11010.09640.0115-0.0358-0.0371-0.0034-0.0030.03290.00150.059321.87462.4558.895
80.44880.5477-0.11571.4695-0.8362.2452-0.0357-0.06780.03050.26190.03730.0527-0.15380.057-0.0015-0.02850.01130.02120.0223-0.01120.064624.39966.43119.327
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A423 - 436
2X-RAY DIFFRACTION2A437 - 473
3X-RAY DIFFRACTION3A474 - 489
4X-RAY DIFFRACTION4A490 - 507
5X-RAY DIFFRACTION5A508 - 522
6X-RAY DIFFRACTION6A523 - 568
7X-RAY DIFFRACTION7A569 - 605
8X-RAY DIFFRACTION8A606 - 628

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