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- PDB-6x6r: Crystal structure of C.difficile ribosyltransferase CDTa in compl... -

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Basic information

Entry
Database: PDB / ID: 6x6r
TitleCrystal structure of C.difficile ribosyltransferase CDTa in complex with pCl-phenylthioDADMeImmA
ComponentsADP-ribosyltransferasePoly (ADP-ribose) polymerase
KeywordsTOXIN / TRANSFERASE / ADP-ribosyltransferase
Function / homologyBinary exotoxin A, clostridial type / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / extracellular region / Chem-4CT / Chem-AR6 / CdtA
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPozharski, E.
CitationJournal: To Be Published
Title: Crystal structure of C.difficile ribosyltransferase CDTa in complex with pCl-phenylthioDADMeImmA
Authors: Pozharski, E.
History
DepositionMay 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 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: ADP-ribosyltransferase
B: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8925
Polymers96,5532
Non-polymers1,3393
Water9,224512
1
A: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6662
Polymers48,2761
Non-polymers3901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2263
Polymers48,2761
Non-polymers9492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.442, 76.066, 100.227
Angle α, β, γ (deg.)90.000, 122.100, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-69-

TYR

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Components

#1: Protein ADP-ribosyltransferase / Poly (ADP-ribose) polymerase


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-4CT / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol


Mass: 389.902 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20ClN5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium Sodium tartrate, 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: Mar 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.01→38.36 Å / Num. obs: 63872 / % possible obs: 98.1 % / Redundancy: 5.3 % / CC1/2: 0.977 / Net I/σ(I): 7.8
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 4072 / CC1/2: 0.319

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6x41

6x41


Resolution: 2.02→38.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.167 / SU Rfree Blow DPI: 0.144 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3089 4.87 %RANDOM
Rwork0.172 ---
obs0.174 63465 98.1 %-
Displacement parametersBiso max: 139.69 Å2 / Biso mean: 46.07 Å2 / Biso min: 18.49 Å2
Baniso -1Baniso -2Baniso -3
1--5.9375 Å20 Å21.2236 Å2
2--5.5458 Å20 Å2
3---0.3917 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 2.02→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6741 0 87 525 7353
Biso mean--50.4 51.3 -
Num. residues----831
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2585SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1208HARMONIC5
X-RAY DIFFRACTIONt_it7095HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion924SEMIHARMONIC5
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_contact8558SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7095HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9605HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion17.18
LS refinement shellResolution: 2.02→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2532 60 4.72 %
Rwork0.2397 1210 -
all0.2404 1270 -
obs--83.44 %
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)
11.30320.01580.10920.9067-0.19181.6857-0.0634-0.093-0.1501-0.03080.0737-0.02340.47470.2066-0.01030.05040.10810.0171-0.1429-0.0049-0.1034-7.9387-41.548530.0918
21.1733-0.77670.00641.6542-0.1920.98850.0880.23890.2223-0.1804-0.0828-0.20.03080.3038-0.0052-0.11350.04020.01120.01470.0044-0.0468-0.5134-15.815415.1107
31.2779-0.20350.02191.7307-0.12731.7218-0.0318-0.10040.29580.0222-0.033-0.0546-0.1696-0.08880.0648-0.06210.0259-0.0033-0.1491-0.0287-0.0439-37.64092.222719.6539
40.8196-0.16360.33552.2109-0.25580.97520.0307-0.03290.0176-0.0891-0.03310.19770.1678-0.2170.0025-0.0003-0.06970.0132-0.0647-0.0197-0.0963-45.1984-27.634117.3897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|213 }A5 - 213
2X-RAY DIFFRACTION2{ A|214 - A|420 }A214 - 420
3X-RAY DIFFRACTION3{ B|6 - B|215 }B6 - 215
4X-RAY DIFFRACTION4{ B|216 - B|420 }B216 - 420

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