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- PDB-8bat: Geobacter lovleyi NADAR -

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Basic information

Entry
Database: PDB / ID: 8bat
TitleGeobacter lovleyi NADAR
ComponentsGeobacter lovleyi NADAR
KeywordsHYDROLASE / TOXIN-ANTITOXIN / DNA ADP-RIBOSYLATION / DNA binding / ANTITOXIN
Function / homology: / DarT1-associated NADAR antitoxin / Uncharacterized protein
Function and homology information
Biological speciesTrichlorobacter lovleyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / 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: Geobacter lovleyi NADAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7423
Polymers28,6451
Non-polymers982
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-5 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.279, 81.597, 86.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Geobacter lovleyi NADAR


Mass: 28644.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichlorobacter lovleyi (bacteria) / Strain: ATCC BAA-1151 / DSM 17278 / SZ / Gene: Glov_2583 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: B3E6E9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% (w/v) PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.3→59.468 Å / Num. obs: 12984 / % possible obs: 100 % / Redundancy: 5.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.087 / Rrim(I) all: 0.21 / Net I/σ(I): 6.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.475 / Mean I/σ(I) obs: 1 / Num. unique obs: 1242 / CC1/2: 0.557 / Rpim(I) all: 0.699 / Rrim(I) all: 1.636 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 2.3→59.468 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 16.205 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.266 / ESU R Free: 0.212
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2321 613 4.731 %
Rwork0.1807 12344 -
all0.183 --
obs-12957 99.931 %
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: 43.149 Å2
Baniso -1Baniso -2Baniso -3
1--2.891 Å2-0 Å2-0 Å2
2--0.865 Å2-0 Å2
3---2.026 Å2
Refinement stepCycle: LAST / Resolution: 2.3→59.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 5 124 1878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121804
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161662
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.6442437
X-RAY DIFFRACTIONr_angle_other_deg0.6151.5613883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.00656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78110327
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.4741080
X-RAY DIFFRACTIONr_chiral_restr0.0790.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02365
X-RAY DIFFRACTIONr_nbd_refined0.2190.2348
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21536
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2892
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2112
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.140.212
X-RAY DIFFRACTIONr_nbd_other0.1980.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.25
X-RAY DIFFRACTIONr_mcbond_it4.1433.719879
X-RAY DIFFRACTIONr_mcbond_other4.1413.718879
X-RAY DIFFRACTIONr_mcangle_it5.7775.5471098
X-RAY DIFFRACTIONr_mcangle_other5.785.5541099
X-RAY DIFFRACTIONr_scbond_it5.114.118925
X-RAY DIFFRACTIONr_scbond_other5.1074.121926
X-RAY DIFFRACTIONr_scangle_it7.3495.9671337
X-RAY DIFFRACTIONr_scangle_other7.3465.971338
X-RAY DIFFRACTIONr_lrange_it8.88445.2972075
X-RAY DIFFRACTIONr_lrange_other8.8844.6312057
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
2.3-2.3590.303390.3138930.3129330.9060.90899.89280.314
2.359-2.4240.356430.3038700.3059140.8940.91799.89060.304
2.424-2.4940.31400.298480.2918900.9090.92199.77530.289
2.494-2.570.297470.2718100.2738570.9120.9391000.264
2.57-2.6550.303440.2358010.2388460.9470.95799.88180.23
2.655-2.7480.305440.2217620.2258060.9430.9661000.212
2.748-2.8510.296370.2057570.2097940.9430.9721000.19
2.851-2.9670.267390.1677070.1717460.9580.9831000.151
2.967-3.0990.157300.1647140.1647440.9880.9851000.146
3.099-3.250.225310.1626640.1656950.9750.9831000.143
3.25-3.4250.258370.1666280.176650.9610.9831000.15
3.425-3.6320.171250.1656090.1656340.9760.9841000.152
3.632-3.8810.255320.1585720.1636040.9580.9861000.143
3.881-4.1910.172280.155340.1515640.9810.98699.64540.138
4.191-4.5890.183170.1325010.1345180.9760.9891000.122
4.589-5.1270.166210.1164510.1194720.9840.9921000.109
5.127-5.9120.204180.1264120.1294300.9780.9911000.117
5.912-7.2230.183160.1583480.1593640.980.9851000.148
7.223-10.1410.189120.1462890.1473010.9780.9861000.144
10.141-59.4680.235130.2741740.271880.9720.94699.46810.276
Refinement TLS params.Method: refined / Origin x: 16.1348 Å / Origin y: -18.8329 Å / Origin z: -17.664 Å
111213212223313233
T0.0184 Å20.031 Å20.0062 Å2-0.065 Å20.0162 Å2--0.0103 Å2
L1.2356 °20.0584 °20.0195 °2-0.9645 °20.3169 °2--0.844 °2
S0.1118 Å °0.1989 Å °0.0136 Å °-0.0757 Å °-0.0964 Å °-0.0449 Å °0.0044 Å °-0.0009 Å °-0.0154 Å °
Refinement TLS groupSelection: ALL

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