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- PDB-1xqp: Crystal structure of 8-oxoguanosine complexed Pa-AGOG, 8-oxoguani... -

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Basic information

Entry
Database: PDB / ID: 1xqp
TitleCrystal structure of 8-oxoguanosine complexed Pa-AGOG, 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum
Components8-oxoguanine DNA glycosylase
KeywordsLYASE / Helix-hairpin-Helix / 8-oxoguanine DNA glycosylase / Archaea / P.aerophilum / Pa-AGOG-8-oxoguanosine complex / DNA repair
Function / homology
Function and homology information


oxidized base lesion DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair
Similarity search - Function
N-glycosylase/DNA lyase-like / N-glycosylase/DNA lyase / N-glycosylase/DNA lyase / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / Helix-hairpin-helix, base-excision DNA repair, C-terminal / Endonuclease III; domain 1 / DNA glycosylase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2'-DEOXY-8-OXOGUANOSINE / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.69 Å
AuthorsLingaraju, G.M. / Sartori, A.A. / Kostrewa, D. / Prota, A.E. / Jiricny, J. / Winkler, F.K.
Citation
Journal: Structure / Year: 2005
Title: A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure
Authors: Lingaraju, G.M. / Sartori, A.A. / Kostrewa, D. / Prota, A.E. / Jiricny, J. / Winkler, F.K.
#1: Journal: To be Published
Title: A novel highly thermostable 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum
Authors: Sartori, A.A. / Lingaraju, G.M. / Hunziker, P. / Winkler, F.K. / Jiricny, J.
History
DepositionOct 13, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Experimental preparation
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 8-oxoguanine DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0783
Polymers29,5111
Non-polymers5662
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.220, 98.110, 36.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-258-

8HG

DetailsThe biologically active unit is a monomer.

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Components

#1: Protein 8-oxoguanine DNA glycosylase


Mass: 29511.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: Pa-AGOG / Plasmid: pET28C(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8ZVK6
#2: Chemical ChemComp-8HG / 2'-DEOXY-8-OXOGUANOSINE


Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, HEPES-NaOH, NaCl, Dithio threitol, Dimethyl sulfoxide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 14, 2003 / Details: Osmic mirrors
RadiationMonochromator: Osmic Mirros / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→57.74 Å / Num. all: 28623 / Num. obs: 28623 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.054 / Net I/σ(I): 17
Reflection shellResolution: 1.69→1.8 Å / Redundancy: 6.12 % / Mean I/σ(I) obs: 3.47 / Num. unique all: 4548 / Rsym value: 0.578 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
MAR345data collection
XDSdata scaling
PHASESphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.69→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.829 / SU ML: 0.084 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22479 1452 5.1 %RANDOM
Rwork0.18258 ---
all0.18467 27180 --
obs0.18467 27180 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.831 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.56 Å2
Refine analyze
FreeObs
Luzzati sigma a0.114 Å0.115 Å
Refinement stepCycle: LAST / Resolution: 1.69→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 40 227 2316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222153
X-RAY DIFFRACTIONr_bond_other_d0.0010.022037
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9872925
X-RAY DIFFRACTIONr_angle_other_deg1.42834706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0365252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.61521.85697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17115378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8311525
X-RAY DIFFRACTIONr_chiral_restr0.1560.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_nbd_refined0.2080.2409
X-RAY DIFFRACTIONr_nbd_other0.1750.21813
X-RAY DIFFRACTIONr_nbtor_other0.0830.21051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.26
X-RAY DIFFRACTIONr_mcbond_it1.011.51643
X-RAY DIFFRACTIONr_mcbond_other0.2041.5511
X-RAY DIFFRACTIONr_mcangle_it1.12822040
X-RAY DIFFRACTIONr_scbond_it1.93731098
X-RAY DIFFRACTIONr_scangle_it2.7384.5885
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.388 104
Rwork0.304 1830

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