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- PDB-3s57: ABH2 cross-linked with undamaged dsDNA-1 containing cofactors -

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Basic information

Entry
Database: PDB / ID: 3s57
TitleABH2 cross-linked with undamaged dsDNA-1 containing cofactors
Components
  • 5'-D(*CP*TP*GP*TP*CP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3'
  • 5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*TP*GP*AP*CP*A)-3'
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
KeywordsOXIDOREDUCTASE/DNA / protein-DNA complex / Jelly-roll fold / dioxygenase / dsDNA binding / plasma / 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
2-OXOGLUTARIC ACID / : / propane-1-thiol / DNA / DNA (> 10) / DNA oxidative demethylase ALKBH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYi, C. / Chen, B. / Qi, B. / Ramirez, B. / Zhang, W. / Jia, G. / Zhang, L. / Li, C.Q. / Dinner, A.R. / Yang, C.-G. / He, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Duplex interrogation by a direct DNA repair protein in search of base damage
Authors: Yi, C. / Chen, B. / Qi, B. / Zhang, W. / Jia, G. / Zhang, L. / Li, C.J. / Dinner, A.R. / Yang, C.G. / He, C.
History
DepositionMay 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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

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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*CP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3'
C: 5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*TP*GP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2668
Polymers31,8043
Non-polymers4615
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-32 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.966, 60.544, 65.455
Angle α, β, γ (deg.)90.00, 90.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 23267.611 Da / Num. of mol.: 1 / Fragment: dioxygenase domain (UNP RESIDUES 56-258) / Mutation: C67S, C165S, C192S, G169C
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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*CP*TP*GP*TP*CP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3'


Mass: 4231.753 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*TP*GP*AP*CP*A)-3'


Mass: 4304.816 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 343 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-XL3 / propane-1-thiol


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


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 5000, 0.1M sodium chloride, 0.025M magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 56467 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 6 / Num. unique all: 5210 / % possible all: 89.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.708 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20221 2333 5.1 %RANDOM
Rwork0.17506 ---
all0.2205 47435 --
obs0.17646 43675 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.195 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-0.04 Å2
2---0.48 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 566 27 338 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212431
X-RAY DIFFRACTIONr_angle_refined_deg1.4642.253417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1635221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61121.78684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5611518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021700
X-RAY DIFFRACTIONr_nbd_refined0.1960.2975
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21576
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2312
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3640.213
X-RAY DIFFRACTIONr_mcbond_it1.3511.51097
X-RAY DIFFRACTIONr_mcangle_it2.16221746
X-RAY DIFFRACTIONr_scbond_it2.72931700
X-RAY DIFFRACTIONr_scangle_it3.8154.51671
X-RAY DIFFRACTIONr_rigid_bond_restr2.40832797
X-RAY DIFFRACTIONr_sphericity_free4.2273339
X-RAY DIFFRACTIONr_sphericity_bonded6.62432310
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 160 -
Rwork0.16 3158 -
obs--95.7 %

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