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- PDB-5an4: Crystal structure of the human 8-oxoguanine glycosylase (OGG1) pr... -

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Basic information

Entry
Database: PDB / ID: 5an4
TitleCrystal structure of the human 8-oxoguanine glycosylase (OGG1) processed with the CrystalDirect automated mounting and cryo-cooling technology
ComponentsN-GLYCOSYLASE/DNA LYASE
KeywordsHYDROLASE / ALLERGEN / PYR/PYL/RCAR / BET V 1 / FLAVONOIDS / AUTOMATED CRYSTAL HARVESTING / AUTOMATED CRYO-COOLING / CRYSTALDIRECT
Function / homology
Function and homology information


Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / negative regulation of double-strand break repair via single-strand annealing / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / oxidized purine nucleobase lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 ...Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / negative regulation of double-strand break repair via single-strand annealing / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / oxidized purine nucleobase lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / response to light stimulus / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / cellular response to cadmium ion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / response to radiation / nuclear matrix / response to estradiol / microtubule binding / endonuclease activity / response to ethanol / response to oxidative stress / damaged DNA binding / mitochondrial matrix / nuclear speck / response to xenobiotic stimulus / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
TATA-Binding Protein - #40 / 8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / HhH-GPD superfamily base excision DNA repair protein / Hypothetical protein; domain 2 / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain ...TATA-Binding Protein - #40 / 8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / HhH-GPD superfamily base excision DNA repair protein / Hypothetical protein; domain 2 / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / Endonuclease III; domain 1 / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.6 Å
AuthorsZander, U. / Ytre-Arne, M. / Dalhus, B. / Hoffmann, G. / Cornaciu, I. / Cipriani, F. / Marquez, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2016
Title: Automated Harvesting and Processing of Protein Crystals Through Laser Photoablation.
Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.A.
History
DepositionSep 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-GLYCOSYLASE/DNA LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2823
Polymers35,0901
Non-polymers1922
Water2,828157
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.071, 106.071, 47.287
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein N-GLYCOSYLASE/DNA LYASE / 8-OXOGUANINE DNA GLYCOSYLASE


Mass: 35089.742 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 12-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O15527, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.8 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM CITRATE, PH=5.5, 0.2 M AMMONIUM SULFATE, 24 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→27 Å / Num. obs: 40235 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.08

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Processing

SoftwareName: REFMAC / Version: 5.8.0123 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.6→26.52 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.84 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21427 1934 4.8 %RANDOM
Rwork0.18362 ---
obs0.1851 38279 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.633 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 10 157 2586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192496
X-RAY DIFFRACTIONr_bond_other_d0.0060.022281
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.943407
X-RAY DIFFRACTIONr_angle_other_deg1.10135220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3422.92113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92315369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6721519
X-RAY DIFFRACTIONr_chiral_restr0.1270.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212859
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02612
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8551.7271247
X-RAY DIFFRACTIONr_mcbond_other1.8551.7261246
X-RAY DIFFRACTIONr_mcangle_it2.6172.591557
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8931.9451249
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 154 -
Rwork0.238 2807 -
obs--99.93 %

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