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- PDB-8k62: Crystal structure of ALKBH1 and 13h complex. -

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Basic information

Entry
Database: PDB / ID: 8k62
TitleCrystal structure of ALKBH1 and 13h complex.
ComponentsNucleic acid dioxygenase ALKBH1
KeywordsDNA BINDING PROTEIN / inhibitor / DNA 6mA demethylase / complex
Function / homology
Function and homology information


positive regulation of gene expression, epigenetic / regulation of translational initiation by tRNA modification / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / regulation of translational elongation / tRNA demethylase activity / oxidative RNA demethylation / regulation of mitochondrial translation / tRNA wobble cytosine modification / DNA oxidative demethylase ...positive regulation of gene expression, epigenetic / regulation of translational initiation by tRNA modification / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / regulation of translational elongation / tRNA demethylase activity / oxidative RNA demethylation / regulation of mitochondrial translation / tRNA wobble cytosine modification / DNA oxidative demethylase / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / 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 / RNA repair / 2-oxoglutarate-dependent dioxygenase activity / DNA alkylation repair / regulation of translational initiation / chemoattractant activity / developmental growth / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / neuron migration / ferrous iron binding / euchromatin / placenta development / neuron projection development / in utero embryonic development / negative regulation of neuron apoptotic process / tRNA binding / DNA repair / endoplasmic reticulum / mitochondrion / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Alkylated DNA repair protein AlkB / 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
: / : / Nucleic acid dioxygenase ALKBH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.991 Å
AuthorsLiang, X. / Yinping, G. / Feng, L. / Jiang, Z. / Ke, X. / Shengyong, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81930125 China
CitationJournal: To Be Published
Title: Crystal structure of ALKBH1 and 13h complex
Authors: Liang, X. / Yinping, G. / Ke, X. / Shengyong, Y.
History
DepositionJul 24, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3233
Polymers43,8881
Non-polymers4352
Water75742
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.502, 56.502, 192.135
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Nucleic acid dioxygenase ALKBH1 / Alkylated DNA repair protein alkB homolog 1 / Alpha-ketoglutarate-dependent dioxygenase ABH1 / DNA ...Alkylated DNA repair protein alkB homolog 1 / Alpha-ketoglutarate-dependent dioxygenase ABH1 / DNA 6mA demethylase / DNA N6-methyl adenine demethylase ALKBH1 / DNA lyase ABH1 / DNA oxidative demethylase ALKBH1 / mRNA N(3)-methylcytidine demethylase


Mass: 43887.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH1, ABH, ABH1, ALKBH / Production host: Escherichia coli (E. coli)
References: UniProt: Q13686, 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 ...References: UniProt: Q13686, 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, DNA N6-methyladenine demethylase, DNA-(apurinic or apyrimidinic site) lyase, DNA oxidative demethylase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IAU / 1-[5-[[3-(trifluoromethyloxy)phenyl]methoxy]pyrimidin-2-yl]pyrazole-4-carboxylic acid


Mass: 380.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11F3N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M imidazole, pH7.0, 20% Polyrthylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→47.42 Å / Num. obs: 20666 / % possible obs: 86.9 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.023 / Rrim(I) all: 0.103 / Χ2: 0.89 / Net I/σ(I): 20.5 / Num. measured all: 412841
Reflection shellResolution: 1.99→2.1 Å / % possible obs: 67.8 % / Redundancy: 18.9 % / Rmerge(I) obs: 1.6 / Num. measured all: 44551 / Num. unique obs: 2353 / CC1/2: 0.938 / Rpim(I) all: 0.372 / Rrim(I) all: 1.644 / Χ2: 0.75 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IE2

6ie2


Resolution: 1.991→34.278 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2777 1996 9.81 %
Rwork0.2043 --
obs0.2114 20341 85.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.991→34.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 28 42 2677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142722
X-RAY DIFFRACTIONf_angle_d1.3373680
X-RAY DIFFRACTIONf_dihedral_angle_d16.2381607
X-RAY DIFFRACTIONf_chiral_restr0.061374
X-RAY DIFFRACTIONf_plane_restr0.01477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.991-2.04040.42351590.37921509X-RAY DIFFRACTION99
2.0404-2.09560.3874560.331506X-RAY DIFFRACTION33
2.0956-2.15720.35371670.29561485X-RAY DIFFRACTION99
2.1572-2.22680.38931520.28261412X-RAY DIFFRACTION99
2.2268-2.30640.3715950.2516828X-RAY DIFFRACTION95
2.3064-2.39870.33261620.2671512X-RAY DIFFRACTION99
2.3987-2.50790.31291610.24611516X-RAY DIFFRACTION99
2.5079-2.64010.31571640.23111510X-RAY DIFFRACTION99
2.6401-2.80540.30731040.21421000X-RAY DIFFRACTION65
2.8054-3.02190.28411660.23191504X-RAY DIFFRACTION100
3.0219-3.32580.2741670.21281546X-RAY DIFFRACTION100
3.3258-3.80650.28931210.18631122X-RAY DIFFRACTION74
3.8065-4.79370.23671510.161387X-RAY DIFFRACTION91
4.7937-34.20.22451710.16381508X-RAY DIFFRACTION98

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