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- PDB-6l94: The structure of the dioxygenase ABH1 from mouse -

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Basic information

Entry
Database: PDB / ID: 6l94
TitleThe structure of the dioxygenase ABH1 from mouse
ComponentsNucleic acid dioxygenase ALKBH1
KeywordsOXIDOREDUCTASE / dioxygenase / ABH1 / demethylation / RNA BINDING PROTEIN
Function / homology
Function and homology information


regulation of translational initiation by tRNA modification / DNA N6-methyladenine demethylase / tRNA wobble cytosine modification / 5-methylcytosine dioxygenase activity / tRNA demethylase activity / regulation of translational elongation / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase / : ...regulation of translational initiation by tRNA modification / DNA N6-methyladenine demethylase / tRNA wobble cytosine modification / 5-methylcytosine dioxygenase activity / tRNA demethylase activity / regulation of translational elongation / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / 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 alkylation repair / 2-oxoglutarate-dependent dioxygenase activity / oxidative demethylation / DNA demethylation / 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 / ferrous iron binding / neuron migration / euchromatin / neuron projection development / regulation of gene expression / negative regulation of neuron apoptotic process / in utero embryonic development / tRNA binding / cell differentiation / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.10012342058 Å
AuthorsXie, W. / Wang, C. / Li, H. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31700625 China
CitationJournal: Biochem Pharmacol / Year: 2021
Title: ALKBH1 promotes lung cancer by regulating m6A RNA demethylation.
Authors: Li, H. / Zhang, Y. / Guo, Y. / Liu, R. / Yu, Q. / Gong, L. / Liu, Z. / Xie, W. / Wang, C.
History
DepositionNov 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 1.2Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4772
Polymers45,4211
Non-polymers561
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-13 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.202, 103.202, 86.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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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 / tRNA N1-methyl adenine demethylase


Mass: 45420.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Alkbh1, Abh, Alkbh / Production host: Escherichia coli (E. coli)
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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15-19% PEG 3350, 0.1 M Na-citrate pH 5.5, 0.1 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→21.18 Å / Num. obs: 8262 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 54.5456975433 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.188 / Net I/σ(I): 7.6
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / Num. unique obs: 1216 / CC1/2: 0.746 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XEG

5xeg


Resolution: 3.10012342058→21.1784838976 Å / SU ML: 0.521279636406 / Cross valid method: FREE R-VALUE / σ(F): 1.33788067498 / Phase error: 38.5031686702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.296891754831 422 5.11143410853 %
Rwork0.278302554478 7834 -
obs0.279383755835 8256 99.818643453 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.8853577906 Å2
Refinement stepCycle: LAST / Resolution: 3.10012342058→21.1784838976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 1 1 2358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00404529750182428
X-RAY DIFFRACTIONf_angle_d0.6596309753163307
X-RAY DIFFRACTIONf_chiral_restr0.0423040300987357
X-RAY DIFFRACTIONf_plane_restr0.00516673993242435
X-RAY DIFFRACTIONf_dihedral_angle_d15.81191443011417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1002-3.54690.3599563566071270.3398265357742615X-RAY DIFFRACTION99.9271137026
3.5469-4.46180.3164005103891220.2843065427042623X-RAY DIFFRACTION99.9271933018
4.4618-21.1780.2674816376121730.2443133130782596X-RAY DIFFRACTION99.6043165468
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)
10.375793850498-0.2862400931860.1483603266680.218921272609-0.1674688457090.436019370805-0.0924373374907-0.006926797762880.0744617065129-0.132022176066-0.06533365577210.0166230903535-0.00248745353327.32507252644E-5-0.1138170211150.708002497670.00904326134054-0.5962565662780.7831306376420.2672955572131.2936008488713.185861726650.6079976424-13.3743653584
21.41865574838-0.10366376369-0.8555001017671.384576171430.2683773979721.92509127188-0.3677912915490.244515854387-0.1302863258260.133178851393-0.269300105220.2775987855510.0423178501778-0.1003205484830.1982354204860.545944556218-0.29960654456-0.3373929702320.6526383739340.3986397284211.2142832818410.764568003735.7877620875-1.3799612316
30.9998270611160.0428993278431-1.34222203471.76142060522-0.2986633116372.336837644020.0338831002104-0.330016324915-0.06585256737840.193297643378-0.03310472134780.224986078865-0.07570174702120.06122482003230.007889115091860.5504815081550.0008759486103080.443210602140.5194469555050.2710031124940.60283238030524.602784066345.561535106811.7291108222
41.373931060770.229983152416-0.2044651073231.02682278471-0.03205691031720.950361083360.000532607743981-0.2763596287120.3810930915480.3486913541380.2996560074730.265222963996-0.2694909538410.120832366383-0.1229170092230.488901847460.0229252245960.101976334620.3931742823840.1584839740.13116014450432.120643971753.864624871410.3479344273
50.949460498322-0.4664447011290.01677130883710.843216074370.1758416634280.610667129221-0.2944495033180.3037707003340.0496452745533-0.01176439703140.3405235896290.6363919000310.01219527072450.141541667552-0.01437773014520.276922593032-0.125441020299-0.08077275513670.3481890120840.1237986341680.38087499629628.320264436339.5182243456-1.43089543798
61.6560709901-0.5222824488250.7992192164570.93650396898-0.3416997472040.7740131985620.05189880855540.2634513068810.114440583334-0.1995722859450.2417509666250.4210739825280.0369584020086-0.1597285565440.1210340449940.235339195769-0.0559706499808-0.5895627995410.5610985781850.3611603971421.0289023690217.99250247947.4259603119-8.20204744148
70.97722103957-0.3754753600690.08323855954750.5163550350180.3267092125840.5015117502630.0332545368911-0.01831886531040.2199846835280.219737269504-0.08047866562220.0199074958238-0.179204634411-0.118299019628-0.1843294329410.892636586730.04603308233460.6016841209860.8312742717780.3429180613231.0224596560710.808788836741.247518908814.8403150989
80.939891096636-0.1259784899020.4748021423770.534682406067-0.4874969866930.9490722702530.285915509016-0.07587269661410.2242831848380.2579878744440.2215243781460.5171156327-0.0281449123205-0.0326132623443-0.1905283063910.176400208550.0267043787430.08135967546940.335234431915-0.0005853541557940.77387550746825.810913440843.85787552333.72055564927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 179 )
5X-RAY DIFFRACTION5chain 'A' and (resid 180 through 241 )
6X-RAY DIFFRACTION6chain 'A' and (resid 242 through 302 )
7X-RAY DIFFRACTION7chain 'A' and (resid 303 through 323 )
8X-RAY DIFFRACTION8chain 'A' and (resid 324 through 356 )

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