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- PDB-3h8o: Structure determination of DNA methylation lesions N1-meA and N3-... -

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Basic information

Entry
Database: PDB / ID: 3h8o
TitleStructure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system
Components
  • 5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(MA7)P*GP*CP*G)-3'
  • 5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3'
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
KeywordsOXIDOREDUCTASE/DNA / protein-DNA complex / Dioxygenase / DNA damage / DNA repair / Iron / Metal-binding / Nucleus / Oxidoreductase / Oxidoreductase-dna COMPLEX
Function / homology
Function and homology information


cytosine C-5 DNA demethylase activity / ALKBH2 mediated reversal of alkylation damage / DNA oxidative demethylase / : / broad specificity oxidative DNA demethylase activity / rDNA binding / DNA alkylation repair / oxidative demethylation / DNA demethylation / ferrous iron binding ...cytosine C-5 DNA demethylase activity / ALKBH2 mediated reversal of alkylation damage / DNA oxidative demethylase / : / broad specificity oxidative DNA demethylase activity / rDNA binding / DNA alkylation repair / oxidative demethylation / DNA demethylation / ferrous iron binding / nucleolus / nucleoplasm / nucleus
Similarity search - Function
DNA oxidative demethylase ALKBH2 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA oxidative demethylase ALKBH2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLu, L. / Yi, C. / Jian, X. / Zheng, Q.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system.
Authors: Lu, L. / Yi, C. / Jian, X. / Zheng, G. / He, C.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 4, 2014Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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_comp_id / _struct_conn.ptnr2_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
B: 5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(MA7)P*GP*CP*G)-3'
C: 5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7754
Polymers31,6823
Non-polymers921
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-9 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.110, 79.110, 242.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 / Alkylated DNA repair protein alkB homolog 2 / Oxy DC1


Mass: 23706.096 Da / Num. of mol.: 1 / Fragment: Residues 56-261 / Mutation: C67S, C165S, E175C, C192S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABH2, ALKBH2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6NS38, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: DNA chain 5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(MA7)P*GP*CP*G)-3'


Mass: 4041.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3'


Mass: 3934.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, NaCl, MgCl2, Cacodylate buffer, 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 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 4, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 29726 / Num. obs: 29687 / % possible obs: 99.87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 20 %
Reflection shellResolution: 2→2.05 Å / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0073refinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.235 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 13 / σ(I): 5 / ESU R: 0.144 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1600 5.1 %RANDOM
Rwork0.202 ---
all0.2035 31322 --
obs0.204 29687 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.56 Å2 / Biso mean: 27.682 Å2 / Biso min: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 528 6 195 2379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212376
X-RAY DIFFRACTIONr_angle_refined_deg1.5832.2633348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.821.39279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56915284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1461518
X-RAY DIFFRACTIONr_chiral_restr0.1110.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211632
X-RAY DIFFRACTIONr_mcbond_it0.6521.51042
X-RAY DIFFRACTIONr_mcangle_it1.16421687
X-RAY DIFFRACTIONr_scbond_it1.78331334
X-RAY DIFFRACTIONr_scangle_it2.8324.51660
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 120 -
Rwork0.241 2119 -
all-2239 -
obs--99.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9525-0.9820.4851.972-0.25461.0270.1865-0.27140.11720.1999-0.03930.1469-0.0389-0.0886-0.1471-0.0086-0.0220.0509-0.0636-0.01150.0364-18.53527.2563.991
20.2749-0.3697-0.15320.9361-0.44861.06120.19670.0436-0.171-0.0179-0.0939-0.04050.1234-0.008-0.10290.0499-0.0207-0.05920.044-0.0350.1062-2.29710.9733.951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 258
2X-RAY DIFFRACTION2B259 - 271
3X-RAY DIFFRACTION2C272 - 284

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