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- PDB-3knt: Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine g... -

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Basic information

Entry
Database: PDB / ID: 3knt
TitleCrystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in complex with 15mer DNA containing 8-oxoguanine
Components
  • 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'
  • 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
  • N-glycosylase/DNA lyase
KeywordsHYDROLASE / LYASE/DNA / protein-DNA complex / OGG / HELIX-HAIRPIN-HELIX / GLYCOSYLASE / 8-OXOGUANINE / 8-OXOG / DNA repair / DNA damage / Glycosidase / Multifunctional enzyme / Nuclease / LYASE-DNA complex
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
DNA / DNA (> 10) / 8-oxoguanine DNA glycosylase/AP lyase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFaucher, F. / Doublie, S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The C-terminal Lysine of Ogg2 DNA Glycosylases is a Major Molecular Determinant for Guanine/8-Oxoguanine Distinction.
Authors: Faucher, F. / Wallace, S.S. / Doublie, S.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-glycosylase/DNA lyase
B: N-glycosylase/DNA lyase
C: N-glycosylase/DNA lyase
D: N-glycosylase/DNA lyase
E: 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'
F: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
G: 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'
H: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
I: 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'
J: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
K: 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'
L: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,35116
Polymers136,25912
Non-polymers924
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-glycosylase/DNA lyase
E: 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'
F: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0884
Polymers34,0653
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-31 kcal/mol
Surface area13740 Å2
MethodPISA
3
B: N-glycosylase/DNA lyase
G: 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'
H: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0884
Polymers34,0653
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-26 kcal/mol
Surface area13150 Å2
MethodPISA
4
C: N-glycosylase/DNA lyase
I: 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'
J: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0884
Polymers34,0653
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-28 kcal/mol
Surface area13130 Å2
MethodPISA
5
D: N-glycosylase/DNA lyase
K: 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'
L: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0884
Polymers34,0653
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-33 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.800, 150.030, 90.270
Angle α, β, γ (deg.)90.00, 107.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-glycosylase/DNA lyase / 8-oxoguanine DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase / AP lyase


Mass: 24868.801 Da / Num. of mol.: 4 / Fragment: MjaOGG / Mutation: K129Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: 1451601, MJ0724, ogg / Plasmid: pET-22 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566(fpg-)
References: UniProt: Q58134, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain
5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'


Mass: 4545.949 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#3: DNA chain
5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'


Mass: 4650.021 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG-8000 16%, 0.1M NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 15, 2009 / Details: ADJUSTABLE FOCUS K-B PAIR SI PLUS PT, RH COATINGS
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→19.8 Å / Num. all: 38203 / Num. obs: 37810 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.82 % / Rmerge(I) obs: 0.124 / Rsym value: 0.071 / Net I/σ(I): 12.58
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.01044 / Mean I/σ(I) obs: 1.72 / Num. unique all: 14919 / Rsym value: 0.817 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FHF

3fhf


Resolution: 2.7→19.8 Å / σ(F): 2 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1899 5.02 %random in each twin domains
Rwork0.1883 ---
obs0.1901 37810 99.34 %-
all-38203 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.08 Å2 / ksol: 0.309 e/Å3
Refinement stepCycle: LAST / Resolution: 2.7→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6988 2299 4 35 9326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049675
X-RAY DIFFRACTIONf_angle_d0.98413464
X-RAY DIFFRACTIONf_dihedral_angle_d22.6153870
X-RAY DIFFRACTIONf_chiral_restr0.0681469
X-RAY DIFFRACTIONf_plane_restr0.0021326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7490.3441810.30751910X-RAY DIFFRACTION98
2.749-2.80170.35221010.30941843X-RAY DIFFRACTION98
2.8017-2.85870.353920.29961916X-RAY DIFFRACTION98
2.8587-2.92070.30221260.2831859X-RAY DIFFRACTION98
2.9207-2.98840.337910.26731900X-RAY DIFFRACTION98
2.9884-3.06290.30211040.26031870X-RAY DIFFRACTION98
3.0629-3.14540.26691000.23181883X-RAY DIFFRACTION98
3.1454-3.23760.2529970.23181924X-RAY DIFFRACTION98
3.2376-3.34160.2529930.22311865X-RAY DIFFRACTION98
3.3416-3.46040.2251140.20911889X-RAY DIFFRACTION98
3.4604-3.59820.22431000.19291893X-RAY DIFFRACTION98
3.5982-3.76090.20121120.17921865X-RAY DIFFRACTION98
3.7609-3.95770.2003980.17631902X-RAY DIFFRACTION98
3.9577-4.20350.1807860.16711881X-RAY DIFFRACTION98
4.2035-4.52450.18891080.1511897X-RAY DIFFRACTION98
4.5245-4.97330.1605920.15181896X-RAY DIFFRACTION98
4.9733-5.67810.2338960.16691900X-RAY DIFFRACTION98
5.6781-7.09890.26041030.19161896X-RAY DIFFRACTION98
7.0989-19.84040.1915990.15021928X-RAY DIFFRACTION98

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