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- PDB-3fhf: Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine D... -

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Basic information

Entry
Database: PDB / ID: 3fhf
TitleCrystal structure of Methanocaldococcus jannaschii 8-oxoguanine DNA glycosylase (MjOgg)
ComponentsN-glycosylase/DNA lyase
KeywordsDNA repair / HYDROLASE / LYASE / ogg / helix-hairpin-helix / glycosylase / 8-oxoguanine / 8-oxoG / MjOgg / DNA damage / Glycosidase / Multifunctional enzyme / Nuclease
Function / homology
Function and homology information


hydrolase activity, hydrolyzing N-glycosyl compounds / 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
8-oxoguanine DNA glycosylase/AP lyase Ogg / 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 / HhH-GPD domain / endonuclease III / DNA glycosylase / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
8-oxoguanine DNA glycosylase/AP lyase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.995 Å
AuthorsFaucher, F. / Doublie, S.
CitationJournal: Structure / Year: 2009
Title: Crystal structures of two archaeal 8-oxoguanine DNA glycosylases provide structural insight into guanine/8-oxoguanine distinction.
Authors: Faucher, F. / Duclos, S. / Bandaru, V. / Wallace, S.S. / Doublie, S.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-glycosylase/DNA lyase


Theoretical massNumber of molelcules
Total (without water)25,8261
Polymers25,8261
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.440, 37.840, 75.010
Angle α, β, γ (deg.)90.000, 116.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

21A-333-

HOH

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Components

#1: Protein N-glycosylase/DNA lyase / E.C.3.2.2.-, E.C.4.2.99.18 / MjOgg / 8-oxoguanine DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase / AP lyase


Mass: 25825.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: 1451601, MJ0724, ogg / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: Q58134, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: PEG 4000 30%, 0.1M sodium citrate, 1% b-Mercaptoethanol, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794, 0.9796, 0.97166
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2008 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.971661
ReflectionResolution: 1.995→19.56 Å / Num. all: 29750 / Num. obs: 28691 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.084 / Net I/σ(I): 15.43
Reflection shellResolution: 1.995→2.1 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 8.23 / Num. unique all: 4041 / Rsym value: 0.279 / % possible all: 92.1

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementResolution: 1.995→19.56 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 2736238 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: 1. The Friedel pairs were used in phasing. 2. BULK SOLVENT MODEL USED in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 759 5 %RANDOM
Rwork0.202 ---
all0.217 15485 --
obs0.222 15220 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.01 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 56.48 Å2 / Biso mean: 24.682 Å2 / Biso min: 7.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å20 Å20.39 Å2
2--4.18 Å20 Å2
3----0.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.995→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 0 153 1968
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.422.5
LS refinement shellResolution: 1.995→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 116 4.8 %
Rwork0.227 2310 -
all-2426 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ligand.paramligand.top

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