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- PDB-3f10: Crystal structure of Clostridium Acetobutylicum 8-oxoguanine DNA ... -

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Basic information

Entry
Database: PDB / ID: 3f10
TitleCrystal structure of Clostridium Acetobutylicum 8-oxoguanine DNA glycosylase in complex with 8-oxoguanosine
Components8-oxoguanine-DNA-glycosylase
KeywordsHYDROLASE / LYASE / 8oxog / guanine / 8oxoguanine / ogg / glycosylase / 8-oxoguanine
Function / homology
Function and homology information


oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / damaged DNA binding
Similarity search - Function
TATA-Binding Protein - #260 / 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 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain ...TATA-Binding Protein - #260 / 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 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 / DNA glycosylase / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXY-8-OXOGUANOSINE / DNA-(apurinic or apyrimidinic site) lyase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsFaucher, F. / Doublie, S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural characterization of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase in its apo form and in complex with 8-oxodeoxyguanosine.
Authors: Faucher, F. / Robey-Bond, S.M. / Wallace, S.S. / Doublie, S.
History
DepositionOct 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: 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: 8-oxoguanine-DNA-glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8734
Polymers34,4651
Non-polymers4073
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.500, 138.500, 138.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein 8-oxoguanine-DNA-glycosylase


Mass: 34465.469 Da / Num. of mol.: 1 / Mutation: K222Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CAC2707, CA_C2707 / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566(fpg-)
References: UniProt: Q97FM4, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-8HG / 2'-DEOXY-8-OXOGUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% PEG-4000, 0.1M NaCitrate, 20%isopropanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→19.79 Å / Num. all: 22102 / Num. obs: 20809 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.74 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.101
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 3.14 / Num. measured obs: 11846 / Num. unique all: 1192 / Num. unique obs: 1373 / Rsym value: 0.741 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.47 Å19.79 Å
Translation2.47 Å19.79 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.79 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 0.3 / Data cutoff high absF: 4675706 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1063 5.1 %RANDOM
Rwork0.215 ---
all0.215 20733 --
obs0.215 20733 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.12 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 75.86 Å2 / Biso mean: 35.489 Å2 / Biso min: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 28 112 2560
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 121 5.4 %
Rwork0.256 2119 -
all-2240 -
obs--62 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ligands.paramligands.top

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