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- PDB-8bau: Phytophthora nicotianae var. parasitica NADAR in complex with ADP... -

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Basic information

Entry
Database: PDB / ID: 8bau
TitlePhytophthora nicotianae var. parasitica NADAR in complex with ADP-ribose
ComponentsNADAR domain-containing protein
KeywordsHYDROLASE / TOXIN-ANTITOXIN / DNA ADP-RIBOSYLATION / ADP-ribosyltransferase activity / DNA binding
Function / homologyYbiA-like / NADAR / YbiA-like superfamily / NADAR domain / Tetracycline Repressor; domain 2 / Orthogonal Bundle / Mainly Alpha / Chem-AR6 / NADAR domain-containing protein
Function and homology information
Biological speciesPhytophthora nicotianae var. parasitica (black shank of tobacco agent)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchuller, M. / Ariza, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R007195/1 United Kingdom
CitationJournal: Mol.Cell / Year: 2023
Title: Molecular basis for the reversible ADP-ribosylation of guanosine bases.
Authors: Schuller, M. / Raggiaschi, R. / Mikolcevic, P. / Rack, J.G.M. / Ariza, A. / Zhang, Y. / Ledermann, R. / Tang, C. / Mikoc, A. / Ahel, I.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references / Category: citation / diffrn_source / pdbx_validate_planes
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type
Revision 1.2Jun 19, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_validate_planes
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADAR domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7197
Polymers21,8501
Non-polymers8706
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint12 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.829, 66.593, 72.888
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 NADAR domain-containing protein


Mass: 21849.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora nicotianae var. parasitica (black shank of tobacco agent)
Strain: INRA-310 / Gene: PPTG_15997 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: W2PSB7
#2: 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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Sodium HEPES pH 7.5, 20% (w/v) PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 1.6→49.212 Å / Num. obs: 29538 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.024 / Rrim(I) all: 0.077 / Net I/σ(I): 13
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.8 % / Rmerge(I) obs: 2.128 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1421 / CC1/2: 0.596 / Rpim(I) all: 0.712 / Rrim(I) all: 2.246

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.6→49.212 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.186 / SU B: 5.253 / SU ML: 0.089 / Average fsc free: 0.9335 / Average fsc work: 0.946 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2279 1425 4.834 %
Rwork0.1976 28054 -
all0.199 --
obs-29479 99.959 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.797 Å2
Baniso -1Baniso -2Baniso -3
1--1.493 Å2-0 Å2-0 Å2
2---1.001 Å2-0 Å2
3---2.494 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 56 88 1680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121626
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161447
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.6592183
X-RAY DIFFRACTIONr_angle_other_deg0.6531.5653368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9395190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.578516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09710280
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.3641084
X-RAY DIFFRACTIONr_chiral_restr0.0940.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
X-RAY DIFFRACTIONr_nbd_refined0.2230.2332
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21341
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2814
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2791
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.286
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.22
X-RAY DIFFRACTIONr_nbd_other0.2290.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.213
X-RAY DIFFRACTIONr_mcbond_it2.7442.567757
X-RAY DIFFRACTIONr_mcbond_other2.7442.567757
X-RAY DIFFRACTIONr_mcangle_it3.3433.837945
X-RAY DIFFRACTIONr_mcangle_other3.3413.836946
X-RAY DIFFRACTIONr_scbond_it4.3253.063869
X-RAY DIFFRACTIONr_scbond_other4.3233.065870
X-RAY DIFFRACTIONr_scangle_it6.0824.3791237
X-RAY DIFFRACTIONr_scangle_other6.0794.3831238
X-RAY DIFFRACTIONr_lrange_it7.17336.2641911
X-RAY DIFFRACTIONr_lrange_other7.16935.8431899
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.6-1.6410.3961010.35320150.35521230.8030.84899.67030.355
1.641-1.6860.3061090.33519840.33420940.8630.85699.95220.333
1.686-1.7350.359910.3219560.32120480.840.88599.95120.313
1.735-1.7880.3151200.27518490.27719690.9180.9231000.263
1.788-1.8470.273720.24518300.24619020.9430.9411000.229
1.847-1.9120.254950.21917790.2218740.940.9611000.199
1.912-1.9840.2421020.20416860.20717880.9620.9691000.184
1.984-2.0650.235770.19916700.20117490.9650.97399.88570.179
2.065-2.1560.207900.19115790.19216690.9680.9771000.173
2.156-2.2610.217950.18314950.18515910.9710.97899.93710.167
2.261-2.3830.279530.18914740.19215270.9610.9771000.171
2.383-2.5280.226620.17813770.1814390.9760.9811000.164
2.528-2.7020.223700.18712850.18913550.9710.9781000.174
2.702-2.9170.29560.19312260.19712820.9590.9771000.182
2.917-3.1950.227650.20711190.20811840.9690.9741000.2
3.195-3.570.235360.22110170.22110530.9690.9721000.215
3.57-4.1180.18440.1789260.1789700.9850.9831000.177
4.118-5.0350.16340.1527870.1528210.9880.9891000.154
5.035-7.0840.232340.1916170.1936510.9760.9851000.192
7.084-49.2120.179190.1543830.1554020.9730.9831000.151
Refinement TLS params.Method: refined / Origin x: 17.4572 Å / Origin y: 7.5147 Å / Origin z: 14.1578 Å
111213212223313233
T0.0178 Å2-0.0082 Å2-0.0098 Å2-0.0295 Å20.0283 Å2--0.0886 Å2
L0.5573 °20.2954 °2-0.3963 °2-0.5809 °2-0.0271 °2--0.47 °2
S0.0035 Å °-0.071 Å °-0.0526 Å °-0.0456 Å °0.0388 Å °-0.0056 Å °-0.0369 Å °0.0624 Å °-0.0423 Å °
Refinement TLS groupSelection: ALL

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