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- PDB-7omu: Thermosipho africanus DarTG in complex with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 7omu
TitleThermosipho africanus DarTG in complex with ADP-ribose
ComponentsMacro domain-containing protein
KeywordsTOXIN / TOXIN-ANTITOXIN / DNA ADP-RIBOSYLATION / ADP-RIBOSE / MACRODOMAIN / ADP-ribosyl transferase
Function / homology
Function and homology information


Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / hydrolase activity / DNA binding
Similarity search - Function
ssDNA thymidine ADP-ribosyltransferase, DarT / ssDNA thymidine ADP-ribosyltransferase, DarT / DNA ADP-ribosyl transferase (DarT) domain profile. / : / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / DNA ADP-ribosyl transferase-DNA ADP-ribosyl glycohydrolase fusion protein
Similarity search - Component
Biological speciesThermosipho africanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsAriza, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R007195/1 United Kingdom
CitationJournal: Nature / Year: 2021
Title: Molecular basis for DarT ADP-ribosylation of a DNA base.
Authors: Schuller, M. / Butler, R.E. / Ariza, A. / Tromans-Coia, C. / Jankevicius, G. / Claridge, T.D.W. / Kendall, S.L. / Goh, S. / Stewart, G.R. / Ahel, I.
History
DepositionMay 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 13, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / diffrn_source / pdbx_database_proc
Item: _atom_site.pdbx_tls_group_id / _citation.country ..._atom_site.pdbx_tls_group_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Macro domain-containing protein
BBB: Macro domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5434
Polymers93,4252
Non-polymers1,1192
Water00
1
AAA: Macro domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2722
Polymers46,7121
Non-polymers5591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Macro domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2722
Polymers46,7121
Non-polymers5591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.458, 187.458, 187.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 5 - 387 / Label seq-ID: 23 - 405

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Macro domain-containing protein


Mass: 46712.316 Da / Num. of mol.: 2 / Mutation: E152A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosipho africanus (bacteria) / Gene: H17ap60334_07413 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: K2PFJ6
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
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: 58.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocyanate, 0.1 M TRIS pH 7.5, 8% (w/v) PEG 20,000, 8% (v/v) PEG500MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.96→93.73 Å / Num. obs: 22975 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.024 / Rrim(I) all: 0.078 / Net I/σ(I): 17.3
Reflection shellResolution: 2.96→3.04 Å / Rmerge(I) obs: 1.713 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1690 / CC1/2: 0.533 / Rpim(I) all: 0.545 / Rrim(I) all: 1.799

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M31

5m31


Resolution: 2.96→76.647 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 45.771 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / ESU R Free: 0.4
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2482 1142 5.006 %
Rwork0.2107 21671 -
all0.213 --
obs-22813 99.455 %
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: 102.859 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.96→76.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 72 0 6194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136334
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176210
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.6448570
X-RAY DIFFRACTIONr_angle_other_deg1.0531.58314324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6525748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39822.013318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.951151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1711542
X-RAY DIFFRACTIONr_chiral_restr0.0460.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026904
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021434
X-RAY DIFFRACTIONr_nbd_refined0.1790.21100
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.25580
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22949
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22898
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.284
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1390.28
X-RAY DIFFRACTIONr_nbd_other0.1790.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2690.23
X-RAY DIFFRACTIONr_mcbond_it2.6988.2923004
X-RAY DIFFRACTIONr_mcbond_other2.6968.2913003
X-RAY DIFFRACTIONr_mcangle_it4.68412.4333748
X-RAY DIFFRACTIONr_mcangle_other4.68412.4343749
X-RAY DIFFRACTIONr_scbond_it2.4478.7663330
X-RAY DIFFRACTIONr_scbond_other2.4478.7683331
X-RAY DIFFRACTIONr_scangle_it4.33713.0174822
X-RAY DIFFRACTIONr_scangle_other4.33713.0194823
X-RAY DIFFRACTIONr_lrange_it7.80693.626715
X-RAY DIFFRACTIONr_lrange_other7.80593.6386716
X-RAY DIFFRACTIONr_ncsr_local_group_10.060.0511935
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.060020.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.060020.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.0370.426930.4131535X-RAY DIFFRACTION98.5472
3.037-3.120.443840.3681537X-RAY DIFFRACTION98.3617
3.12-3.2110.387970.3481461X-RAY DIFFRACTION98.7952
3.211-3.3090.337770.3231466X-RAY DIFFRACTION99.2921
3.309-3.4180.369900.3031395X-RAY DIFFRACTION99.3311
3.418-3.5370.266660.2661384X-RAY DIFFRACTION99.3831
3.537-3.6710.281620.2281338X-RAY DIFFRACTION99.5025
3.671-3.820.221560.2081285X-RAY DIFFRACTION99.8511
3.82-3.990.236690.1921242X-RAY DIFFRACTION99.6201
3.99-4.1840.234510.1861173X-RAY DIFFRACTION99.9184
4.184-4.410.15530.151128X-RAY DIFFRACTION99.8309
4.41-4.6770.229600.1651062X-RAY DIFFRACTION100
4.677-4.9990.219400.1611018X-RAY DIFFRACTION99.9056
4.999-5.3980.276430.201966X-RAY DIFFRACTION100
5.398-5.9120.279440.185855X-RAY DIFFRACTION100
5.912-6.6060.25330.191801X-RAY DIFFRACTION100
6.606-7.6220.212310.184699X-RAY DIFFRACTION99.8632
7.622-9.3190.151380.151587X-RAY DIFFRACTION99.8403
9.319-13.1150.149370.149463X-RAY DIFFRACTION100
13.115-76.6470.481180.343276X-RAY DIFFRACTION98.6577
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)
10.50910.21990.27432.40360.76652.2007-0.0167-0.05280.02310.04530.00120.0689-0.0811-0.20270.01550.08230.02260.00690.0267-0.01850.227366.2611-26.839-20.627
22.6443-0.27-0.45491.2809-0.23682.5234-0.00650.10670.2676-0.0014-0.1166-0.0089-0.2274-0.06670.12310.054-0.0173-0.01930.0565-0.06740.271760.2391-42.100810.5449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA5 - 387
2X-RAY DIFFRACTION2ALLBBB5 - 387

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