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- PDB-3btz: Crystal structure of human ABH2 cross-linked to dsDNA -

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Basic information

Entry
Database: PDB / ID: 3btz
TitleCrystal structure of human ABH2 cross-linked to dsDNA
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
  • DNA (5'-D(*AP*GP*GP*TP*GP*AP*(2YR)P*AP*AP*TP*GP*CP*G)-3')
  • DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DTP*DTP*DAP*DTP*DCP*DAP*DCP*DC)-3')
KeywordsOxidoreductase/DNA / protein/DNA interaction / human dioxygenase / cross-link / DNA repair / 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 / oxidative 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 / : / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.2May 21, 2014Group: Other
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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

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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: DNA (5'-D(*AP*GP*GP*TP*GP*AP*(2YR)P*AP*AP*TP*GP*CP*G)-3')
C: DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DTP*DTP*DAP*DTP*DCP*DAP*DCP*DC)-3')


Theoretical massNumber of molelcules
Total (without water)30,9653
Polymers30,9653
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.523, 75.523, 166.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 22977.275 Da / Num. of mol.: 1 / Mutation: C67S, C165S, C192S, E175C
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
#2: DNA chain DNA (5'-D(*AP*GP*GP*TP*GP*AP*(2YR)P*AP*AP*TP*GP*CP*G)-3')


Mass: 4100.766 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DTP*DTP*DAP*DTP*DCP*DAP*DCP*DC)-3')


Mass: 3886.549 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.83 Å3/Da / Density % sol: 67.86 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 8% PEG 4000, 0.1M sodium chloride, 0.05M magnesium chloride, 0.1M cacodylate, 0.004M hexammine cobalt(III) chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2sodium chloride11
3magnesium chloride11
4cacodylateCacodylic acid11
5hexammine cobalt(III) chloride11
6PEG 400012
7sodium chloride12
8magnesium chloride12
9cacodylateCacodylic acid12
10hexammine cobalt(III) chloride12

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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: 3→20 Å / Num. all: 10204 / Num. obs: 10204 / % possible obs: 99.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 27.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 2.4 / Num. unique all: 484 / % 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: 3→20 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.909 / SU B: 41.816 / SU ML: 0.339 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.056 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26216 522 5.1 %RANDOM
Rwork0.23515 ---
obs0.23658 9626 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.913 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2---1.2 Å20 Å2
3---2.39 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 529 0 4 2158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212262
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4282.2453170
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.61721.4178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.42915277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9051518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021551
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.2888
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21438
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3461.51022
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64221626
X-RAY DIFFRACTIONr_scbond_it1.1131574
X-RAY DIFFRACTIONr_scangle_it1.9274.51544
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 49 -
Rwork0.4 664 -
obs--99.58 %
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)
14.5097-2.06181.25945.5344-0.39924.60440.16220.4393-0.4507-0.4022-0.14010.0910.3309-0.4372-0.02210.0095-0.0502-0.0449-0.5925-0.1447-0.062411.874728.988917.435
24.9003-1.53480.32462.4648-2.595213.3738-0.04210.07220.43870.12610.18290.7753-0.8167-2.1339-0.14080.05150.0507-0.036-0.2858-0.15930.1791-3.231943.723414.3142
33.01822.2181-1.23982.1809-2.970815.49770.1047-0.01660.3882-0.29680.08940.5347-0.0454-0.7853-0.1941-0.04520.0082-0.022-0.0467-0.10730.2081-2.847342.909216.9766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC57 - 2581 - 202
2X-RAY DIFFRACTION2BA1 - 131 - 13
3X-RAY DIFFRACTION3CB1 - 131 - 13

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