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- PDB-6x6w: Crystal structure of inactive enzymatic binary toxin component fr... -

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Basic information

Entry
Database: PDB / ID: 6x6w
TitleCrystal structure of inactive enzymatic binary toxin component from Clostridium difficile
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 / CdtA
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsPozharski, E.
CitationJournal: To Be Published
Title: Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile
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
B: ADP-ribosyltransferase


Theoretical massNumber of molelcules
Total (without water)48,2761
Polymers48,2761
Non-polymers00
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.240, 44.470, 78.390
Angle α, β, γ (deg.)90.000, 116.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ADP-ribosyltransferase


Mass: 48276.301 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG MME2K, 0.1M MIB pH7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.89→39.12 Å / Num. obs: 36970 / % possible obs: 96.5 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 7.1
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 4.5 % / Num. unique obs: 1488 / CC1/2: 0.18 / % possible all: 60.8

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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: 1.89→39.12 Å / Cor.coef. Fo:Fc: 0.9305 / Cor.coef. Fo:Fc free: 0.9081 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1831 5 %RANDOM
Rwork0.1921 ---
obs0.1938 36639 95.44 %-
Displacement parametersBiso max: 171.57 Å2 / Biso mean: 25.73 Å2 / Biso min: 7.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.4736 Å20 Å2-2.1043 Å2
2---1.0004 Å20 Å2
3---0.5267 Å2
Refine analyzeLuzzati coordinate error obs: 0.251 Å
Refinement stepCycle: final / Resolution: 1.89→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 0 306 3624
Biso mean---33.55 -
Num. residues----410
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1254SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes103HARMONIC2
X-RAY DIFFRACTIONt_gen_planes490HARMONIC5
X-RAY DIFFRACTIONt_it3441HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion451SEMIHARMONIC5
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_contact4502SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3441HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4657HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion17.27
LS refinement shellResolution: 1.89→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3076 92 5.24 %
Rwork0.2263 1665 -
all0.2305 1757 -
obs--56.78 %

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