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- PDB-4mg2: ALKBH2 F102A cross-linked to undamaged dsDNA -

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Basic information

Entry
Database: PDB / ID: 4mg2
TitleALKBH2 F102A cross-linked to undamaged dsDNA
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
  • DNA-1
  • DNA-2
KeywordsOXIDOREDUCTASE/DNA / Structural Genomics / Enzyme Function Initiative / Center for Eukaryotic Structural Genomics / CESG / Rossmann Fold / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, B. / Gan, J. / Yang, C.G.
CitationJournal: Sci China Chem / Year: 2014
Title: The complex structures of ALKBH2 mutants cross-linked to dsDNA reveal the conformational swing of β-hairpin
Authors: Chen, B. / Gan, J. / Yang, C.G.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Non-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
B: DNA-1
C: DNA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5374
Polymers32,5133
Non-polymers241
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-24 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.997, 129.997, 84.825
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 / Alkylated DNA repair protein alkB homolog 2 / DNA oxidative demethylase ALKBH2 / Oxy DC1


Mass: 23322.709 Da / Num. of mol.: 1 / Mutation: F102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH2, ABH2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NS38, DNA oxidative demethylase
#2: DNA chain DNA-1 /


Mass: 4618.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Source
#3: DNA chain DNA-2 /


Mass: 4572.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Source
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.19 Å3/Da / Density % sol: 61.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 5000, 100mM sodium chloride, 50mM Magnesium chloride, 100mM 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 19224 / Num. obs: 19087 / % possible obs: 99.5 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.3-2.38199.9
2.38-2.59199.9
2.59-2.9199.9
2.9-3.441100
3.44-3.931100
3.93-50197.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 13.713 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 3 / ESU R: 0.261 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27858 983 5.1 %RANDOM
Rwork0.23389 ---
all0.2785 19087 --
obs0.23607 18106 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.325 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.07 Å2-0 Å2
2---0.07 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1565 550 1 30 2146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0172224
X-RAY DIFFRACTIONr_bond_other_d0.0020.021843
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.7063113
X-RAY DIFFRACTIONr_angle_other_deg1.45334242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.4512275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00915266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0191515
X-RAY DIFFRACTIONr_chiral_restr0.1120.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212107
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02533
LS refinement shellResolution: 2.303→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 77 -
Rwork0.309 1312 -
obs--99.5 %
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)
12.32760.8648-0.49221.72560.08951.37370.05650.01810.12220.00290.1362-0.1123-0.2030.0671-0.19280.0898-0.05050.06040.0855-0.02890.064339.1349-36.6023-4.5372
23.1593-0.92373.614.234-3.211614.5409-0.0728-0.30070.1630.04960.3019-0.369-0.202-0.0795-0.22910.1177-0.07810.06390.1149-0.10260.107148.8404-18.90526.0432
35.5975-0.00250.00523.1209-1.34945.57180.0634-0.0621-0.14560.23220.26240.1752-0.98360.2866-0.32580.3482-0.16290.06020.3058-0.15720.152150.8191-18.38776.0862
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 259
2X-RAY DIFFRACTION2B10 - 23
3X-RAY DIFFRACTION3C28 - 40

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