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- PDB-7vjv: Human AlkB homolog ALKBH6 in complex with alpha-katoglutarate and Mn -

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Basic information

Entry
Database: PDB / ID: 7vjv
TitleHuman AlkB homolog ALKBH6 in complex with alpha-katoglutarate and Mn
ComponentsAlpha-ketoglutarate-dependent dioxygenase alkB homolog 6
KeywordsOXIDOREDUCTASE / ALKBH6 / alpha-ketoglutarate / oxidoreductase activity / DNA binding
Function / homology
Function and homology information


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 / dioxygenase activity / focal adhesion / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Alpha-ketoglutarate-dependent dioxygenase alkB homologue 6 / 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.
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Alpha-ketoglutarate-dependent dioxygenase alkB homolog 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMa, L. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural insights into the interactions and epigenetic functions of human nucleic acid repair protein ALKBH6.
Authors: Ma, L. / Lu, H. / Tian, Z. / Yang, M. / Ma, J. / Shang, G. / Liu, Y. / Xie, M. / Wang, G. / Wu, W. / Zhang, Z. / Dai, S. / Chen, Z.
History
DepositionSep 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6703
Polymers27,4691
Non-polymers2012
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-5 kcal/mol
Surface area11730 Å2
Unit cell
Length a, b, c (Å)46.118, 64.407, 88.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 6 / Alkylated DNA repair protein alkB homolog 6


Mass: 27469.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH6, ABH6 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q3KRA9, 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: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 27487 / % possible obs: 98.67 % / Redundancy: 4.5 % / CC1/2: 0.977 / Net I/σ(I): 15
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 2473 / CC1/2: 0.827

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3THP

3thp


Resolution: 1.75→26.417 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.185 / SU B: 2.15 / SU ML: 0.067 / Average fsc free: 0.9336 / Average fsc work: 0.9405 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2068 1372 5.085 %
Rwork0.1901 25609 -
all0.191 --
obs-26981 98.929 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1707 0 10 86 1803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131761
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171654
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.6622408
X-RAY DIFFRACTIONr_angle_other_deg1.3291.573803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3045219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25220.3391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2715264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.991516
X-RAY DIFFRACTIONr_chiral_restr0.080.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02384
X-RAY DIFFRACTIONr_nbd_refined0.2090.2289
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21380
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2815
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2797
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.279
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.24
X-RAY DIFFRACTIONr_nbd_other0.1290.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0550.26
X-RAY DIFFRACTIONr_mcbond_it1.7312.069882
X-RAY DIFFRACTIONr_mcbond_other1.72.065881
X-RAY DIFFRACTIONr_mcangle_it2.5893.0931099
X-RAY DIFFRACTIONr_mcangle_other2.63.0961100
X-RAY DIFFRACTIONr_scbond_it2.5522.281879
X-RAY DIFFRACTIONr_scbond_other2.5522.282878
X-RAY DIFFRACTIONr_scangle_it3.9573.321309
X-RAY DIFFRACTIONr_scangle_other3.9563.3191310
X-RAY DIFFRACTIONr_lrange_it4.73823.8661812
X-RAY DIFFRACTIONr_lrange_other4.71623.7881801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.2561100.2381873X-RAY DIFFRACTION99.4982
1.78-1.7950.158150.261334X-RAY DIFFRACTION93.5657
1.795-1.8440.2431140.2261828X-RAY DIFFRACTION99.7432
1.844-1.8980.269840.2071746X-RAY DIFFRACTION99.4565
1.898-1.9560.225980.1961710X-RAY DIFFRACTION98.6361
1.956-2.020.228760.191680X-RAY DIFFRACTION99.2651
2.02-2.0910.189810.1771636X-RAY DIFFRACTION99.0768
2.091-2.170.188910.1741549X-RAY DIFFRACTION99.3939
2.17-2.2580.192660.1781528X-RAY DIFFRACTION99.3766
2.258-2.3580.216700.181449X-RAY DIFFRACTION99.281
2.358-2.4730.212680.1811398X-RAY DIFFRACTION99.0541
2.473-2.6060.207680.1771322X-RAY DIFFRACTION98.862
2.606-2.7640.169840.1741233X-RAY DIFFRACTION98.4305
2.764-2.9540.266600.181170X-RAY DIFFRACTION98.008
2.954-3.1890.212580.1941111X-RAY DIFFRACTION99.4048
3.189-3.4920.175490.2021034X-RAY DIFFRACTION99.5404
3.492-3.9010.199550.197927X-RAY DIFFRACTION98.8923
3.901-4.4990.173510.16812X-RAY DIFFRACTION98.0682
4.499-5.4950.223440.175699X-RAY DIFFRACTION96.4935
5.495-7.7120.25290.233568X-RAY DIFFRACTION97.8689

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