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- PDB-6ima: Crystal Structure of ALKBH1 without alpha-1 (N37-C369) -

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Basic information

Entry
Database: PDB / ID: 6ima
TitleCrystal Structure of ALKBH1 without alpha-1 (N37-C369)
ComponentsNucleic acid dioxygenase ALKBH1
KeywordsGENE REGULATION / double-stranded beta helix
Function / homology
Function and homology information


regulation of translational initiation by tRNA modification / positive regulation of gene expression, epigenetic / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / regulation of translational elongation / tRNA demethylase activity / tRNA wobble cytosine modification / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase ...regulation of translational initiation by tRNA modification / positive regulation of gene expression, epigenetic / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / regulation of translational elongation / tRNA demethylase activity / tRNA wobble cytosine modification / oxidative RNA demethylation / regulation of mitochondrial translation / 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 / regulation of translational initiation / chemoattractant activity / developmental growth / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / placenta development / neuron migration / euchromatin / ferrous iron binding / neuron projection development / regulation of gene expression / negative regulation of neuron apoptotic process / in utero embryonic development / cell differentiation / tRNA binding / DNA repair / endoplasmic reticulum / mitochondrion / nucleoplasm
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
CITRIC ACID / Nucleic acid dioxygenase ALKBH1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.593 Å
AuthorsZhang, M. / Yang, S. / Zhao, W. / Li, H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500700 China
CitationJournal: Cell Res. / Year: 2020
Title: Mammalian ALKBH1 serves as an N6-mA demethylase of unpairing DNA.
Authors: Zhang, M. / Yang, S. / Nelakanti, R. / Zhao, W. / Liu, G. / Li, Z. / Liu, X. / Wu, T. / Xiao, A. / Li, H.
History
DepositionOct 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleic acid dioxygenase ALKBH1
B: Nucleic acid dioxygenase ALKBH1
C: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9654
Polymers113,7733
Non-polymers1921
Water1,874104
1
A: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1162
Polymers37,9241
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleic acid dioxygenase ALKBH1


Theoretical massNumber of molelcules
Total (without water)37,9241
Polymers37,9241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleic acid dioxygenase ALKBH1


Theoretical massNumber of molelcules
Total (without water)37,9241
Polymers37,9241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)203.064, 56.062, 105.664
Angle α, β, γ (deg.)90.000, 117.890, 90.000
Int Tables number5
Space group name H-MC121

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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 / DNA lyase ABH1 / DNA oxidative demethylase ALKBH1 / tRNA N1-methyl adenine demethylase


Mass: 37924.215 Da / Num. of mol.: 3 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Alkbh1, Abh, Alkbh / Plasmid: pRSFDuet-P3C / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0CB42, 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: P0CB42, 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.35 % / Mosaicity: 0.452 ° / Mosaicity esd: 0.008 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 16% PEG3350, 0.13 M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2017 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.593→50 Å / Num. obs: 62965 / % possible obs: 98.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.047 / Rrim(I) all: 0.113 / Χ2: 0.858 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.645.90.81916240.7160.3670.90.44699.1
2.64-2.695.90.6816240.8150.3040.7470.45899.3
2.69-2.745.90.58915760.8760.2630.6470.46499.4
2.74-2.85.80.50816520.8770.2280.5590.46499.3
2.8-2.865.80.4416370.8850.1980.4840.47899.5
2.86-2.935.80.36216200.9290.1630.3980.48599.1
2.93-35.70.30416100.9440.1380.3350.50398.8
3-3.085.70.2616120.9640.1170.2860.52398.9
3.08-3.175.30.21416010.9680.1020.2380.56198.5
3.17-3.285.10.16316020.9770.0790.1820.57896.7
3.28-3.3960.13616150.9870.0610.1490.66799.1
3.39-3.5360.11916470.9870.0530.1310.75499.5
3.53-3.6960.10316190.9910.0460.1130.85998.8
3.69-3.885.90.08616120.9920.0390.0951.00298.7
3.88-4.135.80.07716430.9930.0350.0841.17399
4.13-4.455.60.06816210.9940.0320.0761.27198.7
4.45-4.895.10.06415980.9940.0320.0721.47496.2
4.89-5.65.90.06916610.9940.0310.0761.52299.2
5.6-7.055.80.07316630.9950.0330.081.67798.6
7.05-505.30.0616800.9960.0280.0671.88497.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3206: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.593→44.332 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 26.07
RfactorNum. reflection% reflection
Rfree0.2391 6145 9.76 %
Rwork0.1903 --
obs0.1951 62965 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.07 Å2 / Biso mean: 57.1791 Å2 / Biso min: 20.84 Å2
Refinement stepCycle: final / Resolution: 2.593→44.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6851 0 13 104 6968
Biso mean--54.65 44.63 -
Num. residues----863
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5927-2.62210.3341820.27731720190290
2.6221-2.6530.34651720.25411994216699
2.653-2.68530.30352150.25691906212199
2.6853-2.71930.33582440.27481844208899
2.7193-2.75510.33571790.26751942212199
2.7551-2.79280.37132000.2661923212399
2.7928-2.83270.28791790.268919472126100
2.8327-2.8750.33542280.249618602088100
2.875-2.91990.29252350.24861899213499
2.9199-2.96770.28592010.2321905210699
2.9677-3.01890.27171950.22631903209899
3.0189-3.07380.29972130.22271902211599
3.0738-3.13290.30152210.23941904212599
3.1329-3.19680.29672110.23221860207198
3.1968-3.26630.28012340.22431846208097
3.2663-3.34230.28022030.21381869207299
3.3423-3.42580.24712140.18871920213499
3.4258-3.51840.28422020.19051956215899
3.5184-3.62190.23381820.18891897207999
3.6219-3.73880.21852170.19441920213799
3.7388-3.87230.22471950.17921874206999
3.8723-4.02730.24882440.17281898214299
4.0273-4.21040.22421950.16821889208499
4.2104-4.43220.19352220.15751906212899
4.4322-4.70960.19411740.14681899207397
4.7096-5.07280.20511830.15141920210398
5.0728-5.58240.19582310.16461871210299
5.5824-6.38810.19482260.18421861208799
6.3881-8.04050.19112110.15991907211898
8.0405-44.33840.19011370.17191878201595

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