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- PDB-6x6x: Crystal structure of enzymatic binary toxin component from Clostr... -

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Basic information

Entry
Database: PDB / ID: 6x6x
TitleCrystal structure of enzymatic binary toxin component from Clostridium difficile in complex with
ComponentsADP-ribosyltransferase
KeywordsTOXIN / TRANSFERASE / RIBOSYLTRANSFERASE / CDTA
Function / homologyBinary exotoxin A, clostridial type / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / extracellular region / Chem-UTG / CdtA
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsPozharski, E.
CitationJournal: To Be Published
Title: Crystal structure of enzymatic binary toxin component from Clostridium difficile in complex with
Authors: Pozharski, E.
History
DepositionMay 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosyltransferase
B: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1598
Polymers96,5532
Non-polymers6076
Water8,179454
1
A: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7525
Polymers48,2761
Non-polymers4764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4073
Polymers48,2761
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.956, 97.706, 106.366
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 ADP-ribosyltransferase


Mass: 48276.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cdtA / Production host: Escherichia coli (E. coli) / References: UniProt: F5B5W8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UTG / N-(2-chlorophenyl)-N'-[(furan-2-yl)methyl]thiourea


Mass: 266.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11ClN2OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium Thiocyanate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.71→40 Å / Num. obs: 96532 / % possible obs: 99.4 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rpim(I) all: 0.042 / Net I/σ(I): 13.1
Reflection shellResolution: 1.71→1.74 Å / Num. unique obs: 4729 / CC1/2: 0.364

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wn4

2wn4


Resolution: 1.71→39.44 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9323 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 4804 4.99 %RANDOM
Rwork0.1952 ---
obs0.1967 96243 98.97 %-
Displacement parametersBiso max: 104.87 Å2 / Biso mean: 29.75 Å2 / Biso min: 10.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.3891 Å20 Å20 Å2
2--1.4981 Å20 Å2
3----2.8872 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.71→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6719 0 25 454 7198
Biso mean--44.23 32.76 -
Num. residues----833
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2519SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes208HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1002HARMONIC5
X-RAY DIFFRACTIONt_it6991HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion915SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8351SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6991HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9456HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion17.32
LS refinement shellResolution: 1.71→1.75 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 349 5.02 %
Rwork0.2278 6600 -
all0.2289 6949 -
obs--97.51 %

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