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- PDB-3bty: Crystal structure of human ABH2 bound to dsDNA containing 1meA th... -

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Basic information

Entry
Database: PDB / ID: 3bty
TitleCrystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
  • DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7)P*DAP*DCP*DTP*DGP*DCP*DG)-3')
  • DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DGP*DTP*DTP*DAP*DTP*DAP*DCP*DA)-3')
KeywordsOxidoreductase/DNA / protein/DNA interaction / human dioxygenase / DNA repair / cross-linking / DNA damage / 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 / 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
propane-1-thiol / DNA / DNA (> 10) / DNA oxidative demethylase ALKBH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsYang, C.-G. / Yi, C. / He, C.
CitationJournal: Nature / Year: 2008
Title: Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
Authors: Yang, C.G. / Yi, C. / Duguid, E.M. / Sullivan, C.T. / Jian, X. / Rice, P.A. / He, C.
History
DepositionDec 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 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 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7)P*DAP*DCP*DTP*DGP*DCP*DG)-3')
C: DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DGP*DTP*DTP*DAP*DTP*DAP*DCP*DA)-3')
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1454
Polymers31,0693
Non-polymers761
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.915, 77.915, 226.040
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: DNA chain DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7)P*DAP*DCP*DTP*DGP*DCP*DG)-3')


Mass: 3981.631 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DGP*DTP*DTP*DAP*DTP*DAP*DCP*DA)-3')


Mass: 3950.598 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 / Alkylated DNA repair protein alkB homolog 2 / Oxy DC1


Mass: 23136.414 Da / Num. of mol.: 1 / Mutation: C67S, C165S, C192S, G169C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: 12q24.11 / Gene: ALKBH2, ABH2 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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
#4: Chemical ChemComp-XL3 / propane-1-thiol


Mass: 76.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% PEG 8000, 0.1M sodium chloride, 0.05M magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2sodium chloride11
3magnesium chloride11
4cacodylate11
5PEG 800012
6sodium chloride12
7magnesium chloride12
8cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 17062 / Num. obs: 17062 / % possible obs: 95.6 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 30
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2.2 / Num. unique all: 860 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.355 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25893 874 5.1 %RANDOM
Rwork0.22337 ---
obs0.22518 16153 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0.88 Å20 Å2
2---1.76 Å20 Å2
3---2.63 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 526 4 124 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212254
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1162.2463159
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6035198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.42921.51979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70315275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1921518
X-RAY DIFFRACTIONr_chiral_restr0.0630.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021543
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1650.2843
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21428
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.251.51024
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4421614
X-RAY DIFFRACTIONr_scbond_it0.68831573
X-RAY DIFFRACTIONr_scangle_it1.1844.51545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 65 -
Rwork0.301 1193 -
obs--99.84 %
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)
16.1267-1.5523-0.66253.6568-0.71793.01010.2065-0.54340.10810.4773-0.0606-0.1879-0.13660.2734-0.1459-0.2302-0.0441-0.0395-0.18580.0621-0.112418.8194-27.15123.4035
20.9374-0.2110.426410.86181.64480.47420.25620.38140.3062-0.3311-0.237-0.149-0.4587-0.1478-0.01910.0038-0.02410.21190.15040.171-0.21173.6317-9.93313.8194
36.0624-0.8191-10.93512.8530.567425.31821.16820.57340.6666-0.0546-0.15580.4516-1.0495-1.1207-1.01240.14410.08490.1721-0.11730.1373-0.11432.9536-12.51632.8262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC56 - 2581 - 203
2X-RAY DIFFRACTION2BA1 - 131 - 13
3X-RAY DIFFRACTION3CB1 - 131 - 13

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