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- PDB-6y0q: Alpha-ketoglutarate-dependent dioxygenase AlkB in complex with Fe... -

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Basic information

Entry
Database: PDB / ID: 6y0q
TitleAlpha-ketoglutarate-dependent dioxygenase AlkB in complex with Fe, AKG and methylated DNA under anaerobic environment using FT-SSX methods
ComponentsAlpha-ketoglutarate-dependent dioxygenase AlkB
KeywordsOXIDOREDUCTASE / iron dependant dioxygenase / DNA repair / 2-oxoglutarate
Function / homology
Function and homology information


response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair / oxidative demethylation / DNA demethylation / dioxygenase activity / ferrous iron binding / DNA repair / 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
2-OXOGLUTARIC ACID / : / Chem-O5W / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRabe, P. / Beale, J.H. / Lang, P.A. / Dirr, A.S. / Leissing, T.M. / Butryn, A. / Aller, P. / Kamps, J.J.A.G. / Axford, D. / McDonough, M.A. ...Rabe, P. / Beale, J.H. / Lang, P.A. / Dirr, A.S. / Leissing, T.M. / Butryn, A. / Aller, P. / Kamps, J.J.A.G. / Axford, D. / McDonough, M.A. / Orville, A.M. / Owen, R. / Schofield, C.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust106244/Z/14/Z United Kingdom
Medical Research Council (United Kingdom)MR/N002679/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/S50676X/1 United Kingdom
CitationJournal: Iucrj / Year: 2020
Title: Anaerobic fixed-target serial crystallography.
Authors: Rabe, P. / Beale, J.H. / Butryn, A. / Aller, P. / Dirr, A. / Lang, P.A. / Axford, D.N. / Carr, S.B. / Leissing, T.M. / McDonough, M.A. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / ...Authors: Rabe, P. / Beale, J.H. / Butryn, A. / Aller, P. / Dirr, A. / Lang, P.A. / Axford, D.N. / Carr, S.B. / Leissing, T.M. / McDonough, M.A. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / Orville, A.M. / Schofield, C.J. / Owen, R.L.
History
DepositionFeb 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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: Alpha-ketoglutarate-dependent dioxygenase AlkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9544
Polymers24,1041
Non-polymers8503
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-16 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.399, 39.078, 40.840
Angle α, β, γ (deg.)78.990, 78.040, 66.880
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase AlkB / Alkylated DNA repair protein AlkB / DNA oxidative demethylase AlkB


Mass: 24103.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: alkB, aidD, b2212, JW2200 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05050, DNA oxidative demethylase
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-O5W / [(3~{S},5~{R})-5-(6-azanyl-1-methyl-purin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] [(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate / [(1~{R},3~{R})-1-(6-azanyl-1-methyl-purin-9-yl)-1-oxidanyl-5-phosphonooxy-pentan-3-yl] [(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate


Mass: 648.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C21H28N7O13P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 25% w/v PEG 3350, 5% v/v glycerol and 200 mM sodium formate

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.75→39.7 Å / Num. obs: 20346 / % possible obs: 99.96 % / Redundancy: 57.57 % / Biso Wilson estimate: 18.3878665427 Å2 / CC1/2: 0.977 / R split: 0.178 / Net I/σ(I): 37.21
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 2.81 / Num. unique obs: 1028 / CC1/2: 0.255 / R split: 0.789 / % possible all: 100
Serial crystallography measurementCollimation: KB mirrors / Source size: 49 µm2
Serial crystallography sample deliveryDescription: fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Anaerobic chip / Sample holding: thin film mylar sandwich

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
GDAdata collection
DIALS1.8data reduction
DIALS1.8data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JHT

4jht


Resolution: 1.75→39.66 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.97
RfactorNum. reflection% reflection
Rfree0.191 1996 9.849 %
Rwork0.162 --
obs0.165 20267 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.32 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 54 136 1721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041652
X-RAY DIFFRACTIONf_angle_d0.7152265
X-RAY DIFFRACTIONf_chiral_restr0.051240
X-RAY DIFFRACTIONf_plane_restr0.004296
X-RAY DIFFRACTIONf_dihedral_angle_d13.509951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.291390.291302X-RAY DIFFRACTION99.72
1.79-1.840.291370.271309X-RAY DIFFRACTION100
1.84-1.90.311500.241298X-RAY DIFFRACTION100
1.9-1.960.251480.221313X-RAY DIFFRACTION100
1.96-2.030.231440.191303X-RAY DIFFRACTION100
2.03-2.110.241380.191299X-RAY DIFFRACTION100
2.11-2.210.211500.171297X-RAY DIFFRACTION100
2.2-2.320.181360.161333X-RAY DIFFRACTION100
2.32-2.470.181450.171267X-RAY DIFFRACTION100
2.47-2.660.191430.171320X-RAY DIFFRACTION100
2.66-2.920.191370.161311X-RAY DIFFRACTION100
2.92-3.350.181440.141301X-RAY DIFFRACTION100
3.35-4.220.151410.121311X-RAY DIFFRACTION100
4.22-39.650.151440.131307X-RAY DIFFRACTION99.86
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)
12.58198148182-0.0978750943736-1.143899514863.982295810430.7050556887546.898078246850.04364754207910.1613492751510.390002303416-0.1913130481080.201722559280.133963285207-0.608825659369-0.51290616545-0.02165376931890.2034983598330.00290348330547-0.007091331514520.1475488789250.01556654289820.2003980785660.92081154618414.3369864947-0.633387131579
21.606524076840.1666665099820.1131461362272.310082622630.2539008890941.24531986268-0.03797488098110.0513510553832-0.140385735193-0.24082921513-0.0321566415148-0.1068210516730.08616293374040.0294629874020.03246113361760.1638647756980.00840629371032-0.0141013306680.139358384607-0.008773940456740.1475826735570.60494534183-6.65934304404-6.76422231883
32.360785393720.04240189894350.1117801076041.746193336550.2771256377932.06387069295-0.103768207568-0.264740141346-0.761863060830.273314099770.001012208055890.08670304844810.330563322054-0.2709987350820.03635261256960.20561342109-0.0221572276071-0.001397971392610.1865329158320.04939849799160.2448464256312.48012396543-12.25088586966.21839667022
41.268641787791.62893102475-1.142487803775.35752164029-2.083753560121.71005723291-0.04305569014380.101095667498-0.0950223105386-0.1282665039290.0209332129239-0.03873677799950.0485558077113-0.0306641930360.05575656018760.1346584761130.0255739361460.01837475111760.156159321053-0.02170760283240.231218673958.87044572775-14.085944955-2.83050121209
50.872628861126-0.9315743460140.0007278532728787.367605811854.795049871084.07739393390.07032827358590.07037082898760.293730435743-0.3415133005510.166744299144-0.733149988985-0.290547035719-0.0287547793003-0.1648175458350.143719474984-0.02604811098530.0337027852180.1684036515870.007726197554110.23359531389812.49147264077.21230445391-3.23806698376
61.84330213232-0.03210435127280.3045866919541.511892851960.1776571602171.532338546480.029841586547-0.12613525334-0.04993543449420.1146243586530.0296577687382-0.09917699119860.06315286924780.0825010655085-0.04315329707670.157701346601-0.00408878464077-0.008014466717030.1393949836410.008376418499350.1334870995081.51030200777-0.1199883694634.4320207527
71.69943657381-0.2160597196540.4813591150931.056067704270.2059674499161.2726162434-0.0622293337477-0.2145912718770.01056880826850.06996957445980.03288760472080.0387899532003-0.0623895651144-0.1833670989670.01255055484720.1703557588680.01774468361990.0004285961116310.1661630876090.004344475161060.157923211885-6.092032755747.793686350281.4733829212
83.958329021680.8638615085561.366989740141.843475413-0.1033017945411.38660721610.0206983868236-0.5308835538430.1830251951530.128829558099-0.0848753066444-0.01559536538020.0747698081587-0.132931738870.0113046495070.1459375669940.00156250792103-0.001882849746560.188076008071-0.009247403190760.189327958232-4.395465923645.123222275389.71597933949
92.042940468510.34769408555-0.6157957012660.68577302333-0.5578830873972.03355343718-0.06015991512850.1773211332550.0767692670916-0.1974040040850.0956120999660.1170257817590.122386040359-0.0864265289563-0.03075862448040.181735649463-0.0128243535928-0.01142888684810.1538349272550.002953495857920.125311224973-8.755962314432.72577875383-14.3116138731
103.74289397686-0.1744509551231.066007181244.10052344573-0.3212520219745.15953875831-0.00865824399244-0.2585402239240.01892557769980.2127942977550.0178383485642-0.227320498534-0.01358614995550.178992153410.03661595259870.1293349115320.001741661273140.0001887789389640.122476397675-0.01263409916650.1407960817323.92428332999-0.688576783091-0.270855581063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 93 )
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 107 )
6X-RAY DIFFRACTION6chain 'A' and (resid 108 through 142 )
7X-RAY DIFFRACTION7chain 'A' and (resid 143 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 189 )
9X-RAY DIFFRACTION9chain 'A' and (resid 190 through 202 )
10X-RAY DIFFRACTION10chain 'A' and (resid 203 through 215 )

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