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- PDB-7nro: Crystal structure of AlkB in complex with manganese and N-(4-((6-... -

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Basic information

Entry
Database: PDB / ID: 7nro
TitleCrystal structure of AlkB in complex with manganese and N-(4-((6-((carboxymethyl)carbamoyl)-5-hydroxypyridin-2-yl)amino)phenyl)-N-oxohydroxylammonium
ComponentsAlpha-ketoglutarate-dependent dioxygenase AlkB
KeywordsOXIDOREDUCTASE / Alpha ketoglutarate and iron dependent oxygenase / DNA Demethylase / inhibitor complex
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
: / Chem-UPW / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsShishodia, S. / Maheswaran, P. / Leissing, T. / Aik, W.S. / McDonough, M.A. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Based Design of Selective Fat Mass and Obesity Associated Protein (FTO) Inhibitors.
Authors: Shishodia, S. / Demetriades, M. / Zhang, D. / Tam, N.Y. / Maheswaran, P. / Clunie-O'Connor, C. / Tumber, A. / Leung, I.K.H. / Ng, Y.M. / Leissing, T.M. / El-Sagheer, A.H. / Salah, E. / ...Authors: Shishodia, S. / Demetriades, M. / Zhang, D. / Tam, N.Y. / Maheswaran, P. / Clunie-O'Connor, C. / Tumber, A. / Leung, I.K.H. / Ng, Y.M. / Leissing, T.M. / El-Sagheer, A.H. / Salah, E. / Brown, T. / Aik, W.S. / McDonough, M.A. / Schofield, C.J.
History
DepositionMar 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 8, 2021Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)24,4923
Polymers24,1041
Non-polymers3882
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-5 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.880, 38.750, 40.250
Angle α, β, γ (deg.)77.600, 75.380, 66.140
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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P05050, DNA oxidative demethylase
#2: Chemical ChemComp-UPW / 2-[[6-[(4-nitrophenyl)amino]-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid


Mass: 333.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.09 Å3/Da / Density % sol: 41.28 % / Description: rhombohedral 150um x 150um x 100 um
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.5, 2mM MnCl2, 0.1M NaCl, 22% w/v PEG 3350, AlkB protein 20mg/ml, 2mM N-(4-((6-((carboxymethyl)carbamoyl)-5-hydroxypyridin-2-yl)amino)phenyl)-N-oxohydroxylammonium, 0.5% v/v DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2019 / Details: K-B mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.25→35.15 Å / Num. obs: 50272 / % possible obs: 92.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.08 Å2 / CC1/2: 0.9935 / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.48
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.0754 / Mean I/σ(I) obs: 12.16 / Num. unique obs: 2464 / CC1/2: 0.9906 / Rpim(I) all: 0.05 / Rrim(I) all: 0.091 / % possible all: 90.82

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia20.6.277data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FDJ

2fdj


Resolution: 1.25→35.15 Å / SU ML: 0.0951 / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 16.1124
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1639 2427 4.83 %
Rwork0.1463 47841 -
obs0.1471 50268 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.88 Å2
Refinement stepCycle: LAST / Resolution: 1.25→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 25 279 1867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01171722
X-RAY DIFFRACTIONf_angle_d1.20432354
X-RAY DIFFRACTIONf_chiral_restr0.0895242
X-RAY DIFFRACTIONf_plane_restr0.0169335
X-RAY DIFFRACTIONf_dihedral_angle_d12.8551658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.1811280.17572728X-RAY DIFFRACTION91.01
1.28-1.30.18451500.16462807X-RAY DIFFRACTION92.23
1.3-1.330.1571470.1612815X-RAY DIFFRACTION92.3
1.33-1.370.16561260.16712810X-RAY DIFFRACTION93.21
1.37-1.40.18751390.1682806X-RAY DIFFRACTION93.08
1.4-1.450.19291610.16242841X-RAY DIFFRACTION93.37
1.45-1.490.17281410.15342834X-RAY DIFFRACTION93.38
1.49-1.550.15451500.14382862X-RAY DIFFRACTION93.69
1.55-1.610.16661280.14632827X-RAY DIFFRACTION93.66
1.61-1.680.17171320.14512836X-RAY DIFFRACTION93.3
1.68-1.770.17411330.15062819X-RAY DIFFRACTION93.06
1.77-1.880.17321580.14432781X-RAY DIFFRACTION92.74
1.88-2.020.14761520.13632824X-RAY DIFFRACTION93.09
2.03-2.230.14031330.12832824X-RAY DIFFRACTION92.84
2.23-2.550.1751340.13292818X-RAY DIFFRACTION93.03
2.55-3.210.15171620.13992815X-RAY DIFFRACTION92.94
3.21-35.150.17041530.15812794X-RAY DIFFRACTION92.67
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)
10.9073006415920.271114986320.4053695504171.77036426532-1.964783089273.29385519363-0.101760890119-0.04063291794270.1693142949540.08401183546520.05901078889490.0574467734676-0.452362600169-0.180928403457-0.02300292781520.1232905881530.00682974312369-0.006964630605440.123918787429-0.004695086306040.154652895422.112426242116.0820668527-3.34945392936
21.38335128891.575907825230.3606195231711.853625807980.4640994691070.121452885187-0.07496033053310.3414429238060.0371994289193-0.5019341588950.0677431039525-0.3057363194630.04698929278210.130343287445-0.02389230720450.1417579613550.003043117708750.02067603113930.15622547033-0.01036599150590.1293236295376.951101578520.599115124017-14.9735495166
30.715429393485-0.3522672718110.07381137328590.58019381850.04764448120780.0703323476307-0.0094201731025-0.251524647288-0.1077061341810.0621037229480.03124971357670.01962996848220.174054287210.0420427472290.1915971353290.143478197642-0.0121037051402-0.003920025086580.130087988866-0.00671104704530.167900634962-4.83083667579-9.96788105683-2.59860129015
41.326694777810.1037564745980.3544508115890.9771436533490.2472341779470.374883165840.122053975115-0.376397547061-0.3730652810570.347779399523-0.07945575896150.05589826317620.364208953663-0.299255185670.02922794595170.187509750111-0.02865112385-0.008165968604910.1728031861680.0215080765190.2014634900613.01074804333-9.230020458612.78311001265
50.0301867102965-0.0258182286923-0.03650043689060.03100596640.001423902593660.0360375917308-0.1007756037920.0445577400889-0.156949937065-0.07383968222510.0489586102786-0.09497743139220.07348893572720.0284414124608-0.0309458567470.114717201990.007412362034250.005222576492550.0903822243601-0.01266775786440.2031491620049.41926080135-11.1772703804-3.93257486614
60.0874069389581-0.246018737747-0.2933242424080.8054639944760.9513243176481.15362914124-0.03125110891390.05766796499230.2304810855450.02916083722670.101870749941-0.248048586693-0.07441033220930.206485681915-0.06032688420570.119506956136-0.01420475223-0.0009484110582670.132844077503-0.01182784184950.16963078419512.9639312328.93498233548-4.64216706193
70.213471655696-0.002668860273890.2187400911371.173899983940.7077393862881.2838460146-0.0414593143864-0.0272698457552-0.06164270067770.1096567471380.124888933691-0.264071969875-0.001828549399240.1625648442250.4759411033180.06855448976870.023270868603-0.03098496452160.04200212689130.01580500153070.06251644367522.041292143892.389053873523.63752565775
80.673021539283-0.02188031819650.1141949529420.596227909623-0.2513056287210.222448354272-0.048993612171-0.1053267398650.08141555587630.1201913579930.06367927510770.0436250161177-0.0730911107909-0.05456971418920.07421988795740.1002557487260.01333032508740.002805580626510.108077259436-0.008100131610950.0920308796982-5.42365222589.697694337961.61236780162
90.005907848359060.0265063138293-0.00415991454440.0132178407916-0.01600606474030.002195667041730.00723694039737-0.1517902824850.02015562842630.0437912507856-0.01033802466640.00822265985042-0.0206722585655-0.0128609139754-0.0002343350240680.1430603323220.00456372011089-0.006341036531720.159252651593-0.00161270306260.115252039537-3.413134930067.51944256269.42199475271
100.187667777660.0642827908255-0.1319210963730.2783586277240.05719173293980.0961336463766-0.036444820096-0.0131302023450.01058727443030.02024600150680.0390474139973-0.02179011598880.0181311869761-0.0414020457216-0.08499222769350.0908463496251-0.00896542927218-0.0118680829870.1093067244350.002774125191120.0843405259417-2.404475080183.26085547842-7.09316728041
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 29 )14 - 291 - 16
22chain 'A' and (resid 30 through 41 )30 - 4117 - 28
33chain 'A' and (resid 42 through 59 )42 - 5929 - 46
44chain 'A' and (resid 60 through 79 )60 - 7947 - 66
55chain 'A' and (resid 80 through 93 )80 - 9367 - 80
66chain 'A' and (resid 94 through 106 )94 - 10681 - 93
77chain 'A' and (resid 107 through 142 )107 - 14294 - 129
88chain 'A' and (resid 143 through 179 )143 - 179130 - 166
99chain 'A' and (resid 180 through 189 )180 - 189167 - 176
1010chain 'A' and (resid 190 through 215 )190 - 215177 - 202

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