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- PDB-6x41: Crystal structure of inactive enzymatic binary toxin component fr... -

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Basic information

Entry
Database: PDB / ID: 6x41
TitleCrystal structure of inactive enzymatic binary toxin component from Clostridium difficile
ComponentsCdtA
KeywordsTOXIN / 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: 2.36 Å
AuthorsPozharski, E.
CitationJournal: To Be Published
Title: Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile
Authors: Pozharski, E.
History
DepositionMay 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CdtA
B: CdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2584
Polymers99,0742
Non-polymers1842
Water4,161231
1
A: CdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6292
Polymers49,5371
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6292
Polymers49,5371
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.116, 114.116, 179.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CdtA


Mass: 49536.766 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Li2SO4, 1.2M NaH2PO4, 0.8M K2HPO4, 0.1M Glycine pH 10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.36→39.36 Å / Num. obs: 49282 / % possible obs: 99.8 % / Redundancy: 5.6 % / CC1/2: 0.991 / Net I/σ(I): 4.6
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 5.7 % / Num. unique obs: 4452 / CC1/2: 0.362 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WN5

2wn5


Resolution: 2.36→33.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.279 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.22
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2452 5.01 %RANDOM
Rwork0.2015 ---
obs0.2037 48979 99.3 %-
Displacement parametersBiso max: 102.71 Å2 / Biso mean: 55.75 Å2 / Biso min: 29.23 Å2
Baniso -1Baniso -2Baniso -3
1-6.3882 Å20 Å20 Å2
2--6.3882 Å20 Å2
3----12.7764 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.36→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6734 0 12 231 6977
Biso mean--64.32 50.81 -
Num. residues----834
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2475SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1170HARMONIC5
X-RAY DIFFRACTIONt_it6927HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion907SEMIHARMONIC5
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_contact5428SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6927HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg9360HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion19.31
LS refinement shellResolution: 2.36→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3654 43 4.39 %
Rwork0.2422 937 -
all0.2478 980 -
obs--87.87 %

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