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- PDB-4mgt: ALKBH2 R110A cross-linked to undamaged dsDNA -

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Basic information

Entry
Database: PDB / ID: 4mgt
TitleALKBH2 R110A cross-linked to undamaged dsDNA
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
  • DNA1
  • DNA2
KeywordsOXIDOREDUCTASE/DNA / protein-DNA complex / 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
DNA / DNA (> 10) / DNA oxidative demethylase ALKBH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 1.1May 28, 2014Group: Non-polymer description
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _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_conn_type.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: DNA1
C: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5704
Polymers31,5463
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-25 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.099, 129.099, 84.466
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 23238.545 Da / Num. of mol.: 1 / Fragment: UNP residues 56-258 / Mutation: R110A
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 DNA1


Mass: 4313.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesis
#3: DNA chain DNA2


Mass: 3993.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesis
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.23 Å3/Da / Density % sol: 61.88 %
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: Feb 10, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionRedundancy: 27.6 % / Number: 369194 / Rmerge(I) obs: 0.101 / Χ2: 1.06 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 13363 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.65099.710.0471.09129.7
4.455.610010.071.00132
3.884.4599.910.0831.09133
3.533.8810010.1241.04633.3
3.283.5399.910.1951.13133.4
3.083.2899.810.2961.132.4
2.933.0899.910.431.00629.5
2.82.9399.710.6041.00524.4
2.692.899.310.830.99417
2.62.6995.110.8941.0469.7
ReflectionResolution: 2.6→50 Å / Num. all: 13880 / Num. obs: 13760 / % possible obs: 99.2 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.8
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.6-2.69195.1
2.69-2.8199.3
2.8-2.93199.7
2.93-3.08199.9
3.08-3.28199.8
3.28-3.53199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S5A

3s5a


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 21.869 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.448 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 649 4.9 %RANDOM
Rwork0.2306 ---
obs0.233 13200 99.38 %-
all-13849 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.4 Å2 / Biso mean: 70.637 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.41 Å2-0 Å2
2--0.41 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 550 1 0 2151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0172271
X-RAY DIFFRACTIONr_bond_other_d0.0010.021886
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.713180
X-RAY DIFFRACTIONr_angle_other_deg0.95434345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.56621.92378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16915274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5351516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 44 -
Rwork0.398 858 -
all-902 -
obs--95.05 %
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)
12.29610.3991-0.44122.02760.06110.82630.0754-0.05270.19470.0060.1311-0.0687-0.08540.0888-0.20650.0893-0.04610.09240.1134-0.01570.143638.5321-35.7958-3.9841
24.0321-2.07942.96214.0644-3.635310.5692-0.051-0.23120.20870.27720.2095-0.2432-0.4956-0.1955-0.15850.1365-0.10770.08640.149-0.11560.115548.5332-18.5386.019
35.2287-0.53770.80774.0922-2.4966.31680.04610.0436-0.07450.22010.09130.04-0.90460.3679-0.13740.3126-0.19640.10690.2411-0.19340.185350.5074-18.05126.0938
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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