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- PDB-7ui4: Crystal structure of the DNA preQ0 insertase DpdA -

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Basic information

Entry
Database: PDB / ID: 7ui4
TitleCrystal structure of the DNA preQ0 insertase DpdA
ComponentsDNA-guanine transglycosylase
KeywordsDNA BINDING PROTEIN / 2'-deoxy-7-cyano-7-deazaguanosine / dPreQ0 / DNA modification / DNA-guanine transglycosylase
Function / homology
Function and homology information


pentosyltransferase activity / tRNA modification
Similarity search - Function
: / Queuine tRNA-ribosyltransferase-like / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
tRNA-guanine transglycosylase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Montevideo (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å
AuthorsHung, S.-H. / Swairjo, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM110588-06A1 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: 7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system.
Authors: Gedara, S.H. / Wood, E. / Gustafson, A. / Liang, C. / Hung, S.H. / Savage, J. / Phan, P. / Luthra, A. / de Crecy-Lagard, V. / Dedon, P. / Swairjo, M.A. / Iwata-Reuyl, D.
History
DepositionMar 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-guanine transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4102
Polymers50,3451
Non-polymers651
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.102, 141.768, 42.496
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA-guanine transglycosylase


Mass: 50344.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Montevideo (bacteria)
Gene: AIG37_01840, APO85_00905, AU259_04380, AVH73_05845, AVH73_21940, AXU14_04585, AXU32_02035, B0D32_05855, B0D32_22885, B5881_18565, B6C67_03300, B6C67_22040, BIW02_04385, BIW02_22200, C2689_ ...Gene: AIG37_01840, APO85_00905, AU259_04380, AVH73_05845, AVH73_21940, AXU14_04585, AXU32_02035, B0D32_05855, B0D32_22885, B5881_18565, B6C67_03300, B6C67_22040, BIW02_04385, BIW02_22200, C2689_01835, C2689_23730, CW117_05915, D0215_03875, D0215_23815, D2K49_10730, DK664_02155, DK664_23285, DPL19_04880, DPL19_23835, DQS63_22335, DT992_19130, DT992_25255, DYO72_07125, DYO72_24190, DYT96_02055, E0U36_08570, E0U36_22475, E4933_05800, E4S88_01055, E4S88_22855, EIC46_05430, FEH78_03570, G2910_01835, G2910_23335, G2911_06635, G2911_23200, G3401_000792, G4B33_001303, G4Y15_003124, G4Y21_000316, G4Y22_001365, G9254_000030, G9254_004691, G9G43_001321, G9G43_004619, II32_05770
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): C41 / References: UniProt: A0A3V8XDB8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: mixing 2 ul sample containing 4.0 mg/ml protein (81.5 uM), 0.5 mM guanine, 50 mM Tris (pH 7.5), 100 mM NaCl and 1 mM DTT with 3 ul reservoir solution containing 10% (w/v) polyethylene glycol ...Details: mixing 2 ul sample containing 4.0 mg/ml protein (81.5 uM), 0.5 mM guanine, 50 mM Tris (pH 7.5), 100 mM NaCl and 1 mM DTT with 3 ul reservoir solution containing 10% (w/v) polyethylene glycol (PEG) 8000, 8% (v/v) ethylene glycol (EG), 100 mM HEPES (pH 7.5), 0.1 mM ZnCl2, 3 mM reduced glutathione (GSH) and 3 mM oxidized glutathione (GSSG)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.28149, 0.98397, 1.28268
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.281491
20.983971
31.282681
ReflectionResolution: 2.51→73.59 Å / Num. obs: 16179 / % possible obs: 87.1 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.029 / Rrim(I) all: 0.107 / Net I/σ(I): 21.8 / Num. measured all: 207845
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.51-2.658.80.9641160013240.920.3411.0252.350.4
7.94-73.5912.10.03582516830.9990.010.03655.899.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.27data extraction
XDSvJan26, 2018data reduction
SOLVE2.13phasing
RefinementMethod to determine structure: MAD / Resolution: 2.51→54.78 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1785 / WRfactor Rwork: 0.1298 / FOM work R set: 0.9054 / SU B: 15.95 / SU ML: 0.144 / SU Rfree: 0.2264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1785 790 4.9 %RANDOM
Rwork0.1298 ---
obs0.1322 15348 87.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.18 Å2 / Biso mean: 55.874 Å2 / Biso min: 34.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å2-0 Å20 Å2
2--1.96 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 2.51→54.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 1 91 3459
Biso mean--57.19 54.48 -
Num. residues----413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0143444
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173004
X-RAY DIFFRACTIONr_angle_refined_deg1.0781.6634644
X-RAY DIFFRACTIONr_angle_other_deg0.8471.6337070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6175412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32720.818220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.21515603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2191536
X-RAY DIFFRACTIONr_chiral_restr0.0540.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023932
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02664
X-RAY DIFFRACTIONr_rigid_bond_restr2.08236448
X-RAY DIFFRACTIONr_sphericity_free44.532549
X-RAY DIFFRACTIONr_sphericity_bonded30.17656414
LS refinement shellResolution: 2.51→2.574 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.421 28 -
Rwork0.273 571 -
obs--45.31 %

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