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

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Basic information

Entry
Database: PDB / ID: 6ypv
TitleAlpha-ketoglutarate-dependent dioxygenase AlkB in complex with Fe and AKG after oxygen exposure using FT-SSX methods
ComponentsAlpha-ketoglutarate-dependent dioxygenase AlkB
KeywordsOXIDOREDUCTASE / iron dependent dioxygenase / DNA repait / 2-oxoglutarate
Function / homology
Function and homology information


response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / oxidative RNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / oxidative RNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm / cytosol
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 / : / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionApr 16, 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)24,3053
Polymers24,1041
Non-polymers2022
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-15 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.037, 39.107, 40.860
Angle α, β, γ (deg.)78.140, 76.040, 66.510
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 (strain K12) (bacteria)
Gene: alkB, aidD, b2212, JW2200 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05050, DNA oxidative demethylase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 25% w/v PEG 3350, 5% v/v glycerol and 200 mM sodium ormate

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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: 2.1→39.35 Å / Num. obs: 11994 / % possible obs: 100 % / Redundancy: 25.8 % / Biso Wilson estimate: 23.04 Å2 / CC1/2: 0.874 / R split: 0.333 / Net I/σ(I): 48.4
Reflection shellResolution: 2.1→2.136 Å / Mean I/σ(I) obs: 8.795 / Num. unique obs: 593 / CC1/2: 0.414 / R split: 0.617
Serial crystallography measurementCollimation: KB mirrors / Source size: 49 µm2
Serial crystallography sample deliveryDescription: fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: FixedTarget Chip

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
GDAdata collection
DIALS1.8data reduction
DIALS1.8data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JHT

4jht


Resolution: 2.1→39.35 Å / SU ML: 0.2596 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.3511
RfactorNum. reflection% reflection
Rfree0.2505 1181 9.99 %
Rwork0.2194 --
obs0.2225 11819 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.83 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 11 72 1573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041566
X-RAY DIFFRACTIONf_angle_d0.53152142
X-RAY DIFFRACTIONf_chiral_restr0.0431229
X-RAY DIFFRACTIONf_plane_restr0.0026289
X-RAY DIFFRACTIONf_dihedral_angle_d14.0146923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20.2881510.2851359X-RAY DIFFRACTION99.93
2.2-2.310.34851460.2551316X-RAY DIFFRACTION99.8
2.31-2.460.28951500.25091321X-RAY DIFFRACTION99.86
2.46-2.650.30251460.25431339X-RAY DIFFRACTION99.73
2.65-2.910.26011490.23821308X-RAY DIFFRACTION99.93
2.91-3.330.2531430.21621320X-RAY DIFFRACTION99.86
3.33-4.20.22111490.18631343X-RAY DIFFRACTION100
4.2-39.350.20691470.19231332X-RAY DIFFRACTION99.93
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)
11.38909533684-0.7457219638321.827919147533.7456133081.000753441797.47143291825-0.1111680505420.148422593870.236688936262-0.04745412208090.175552880057-0.162722698864-0.533837683658-0.45093765139-0.159980821270.196975111199-0.03136297145660.001121100865690.1690730949610.0889524794820.2228245458592.1326858559113.4821699824-3.17775095925
26.291437268931.96352344089-0.4207935561366.57826952922-0.3511156635880.65413974913-0.0253431409122-0.116432572975-0.17081832942-0.277854004095-0.00827834634131-0.01275370478270.03558589630480.02438786338140.04151341050130.1736315907780.00548465721883-0.03533292430620.130182607886-0.009378754828670.1075437999170.507948196543-8.0339445911-6.84188624177
35.507929880391.21699945988-4.48805258375.96224978317-1.112941692497.910837177560.207815140817-0.698275399339-0.9239492471690.588323093098-0.1900770754590.08066761855630.1843239941-0.09904041766130.05240751608190.332933729339-0.0595755012265-0.06933203314130.2636930708580.1150895728630.2842359778393.06877735741-12.0560156225.81168449049
44.527130773654.63676939627-2.899399881047.64148540885-5.330860205534.38777717190.01855580613420.00387734998457-0.0427509713136-0.382982241810.000960565785976-0.2504075801160.0211337874362-0.06742924435160.02833400035930.1472236466180.02793008089180.02263616990490.155773250091-0.03283986821780.2608083400058.83106052006-14.134558749-3.17205400211
52.00489818786-1.25757165808-0.641911928544.344823660615.462338633457.48083099591-0.1374242730320.09142948943230.567526389648-0.4842704264330.482214364676-0.873402395736-0.4546786082060.508668303053-0.3531958019620.16448515806-0.04002175080530.01155495538840.2038790131610.02031804099410.29967683821912.42553012516.7980027716-4.0476520962
63.47471944505-1.94883771087-0.5659819286243.30194241627-0.8458495476361.70866512848-0.0007615097333760.04323966180150.03723292438410.3332647527170.01488571494-0.4013519770290.1836776968220.255476188772-0.02609217668290.1472690937540.009570381545250.01789444678030.1653493759680.02437256944570.1459317624925.948503273181.387897189930.471339211703
72.15319251353-0.04155597304620.5540316043131.335778971210.7319203083912.07894289692-0.0324966086209-0.2880959746550.001439063014060.09493677625050.08556816352270.0490818488865-0.0102526840582-0.174986087524-0.04334971555450.1806258932580.002509856318460.00818326054460.1759868179090.04588292043160.174581102551-4.274601552123.834273223811.29498119868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 93 )
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 123 )
7X-RAY DIFFRACTION7chain 'A' and (resid 124 through 213 )

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