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- PDB-4jht: Crystal Structure of AlkB in complex with 5-carboxy-8-hydroxyquin... -

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Basic information

Entry
Database: PDB / ID: 4jht
TitleCrystal Structure of AlkB in complex with 5-carboxy-8-hydroxyquinoline (IOX1)
ComponentsAlpha-ketoglutarate-dependent dioxygenase AlkB
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / double-stranded beta helix / jelly-roll motif / oxidoreductase / dioxygenase / Nucleic acid demethylase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


response to methyl methanesulfonate / : / DNA oxidative demethylase / : / oxidative RNA demethylation / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair ...response to methyl methanesulfonate / : / DNA oxidative demethylase / : / oxidative RNA demethylation / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair / oxidative demethylation / : / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm
Similarity search - Function
Alkylated DNA repair protein AlkB / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 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. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
8-hydroxyquinoline-5-carboxylic acid / ACETATE ION / : / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous Replacement / Resolution: 1.18 Å
AuthorsAik, W.S. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2013
Title: 5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation.
Authors: Hopkinson, R.J. / Tumber, A. / Yapp, C. / Chowdhury, R. / Aik, W. / Che, K.H. / Li, X.S. / Kristensen, J.B.L. / King, O.N.F. / Chan, M.C. / Yeoh, K.K. / Choi, H. / Walport, L.J. / Thinnes, C. ...Authors: Hopkinson, R.J. / Tumber, A. / Yapp, C. / Chowdhury, R. / Aik, W. / Che, K.H. / Li, X.S. / Kristensen, J.B.L. / King, O.N.F. / Chan, M.C. / Yeoh, K.K. / Choi, H. / Walport, L.J. / Thinnes, C.C. / Bush, J.T. / Lejeune, C. / Rydzik, A.M. / Rose, N.R. / Bagg, E.A. / McDonough, M.A. / Krojer, T. / Yue, W.W. / Ng, S.S. / Olsen, L. / Brennan, P.E. / Oppermann, U. / Muller-Knapp, S. / Klose, R.J. / Ratcliffe, P.J. / Schofield, C.J. / Kawamura, A.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 25, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)23,3275
Polymers22,9451
Non-polymers3814
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.839, 38.848, 40.450
Angle α, β, γ (deg.)77.620, 75.010, 66.100
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 22945.236 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 12-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aidD, alkB, b2212, JW2200 / Plasmid details: PIR1 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05050, DNA oxidative demethylase

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Non-polymers , 5 types, 273 molecules

#2: Chemical ChemComp-8XQ / 8-hydroxyquinoline-5-carboxylic acid


Mass: 189.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7NO3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.37 % / Mosaicity: 0.508 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23% PEG 3350, 0.264M NaCl, 0.1M HEPES pH7.5, 1mM 8XQ, 1mM MnCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. all: 64400 / Num. obs: 60068 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.036 / Net I/σ(I): 17.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.18-1.223.10.3333.855130.94185.7
1.22-1.273.50.2945.357761.02689.9
1.27-1.333.80.2377.359231.09892.1
1.33-1.43.90.1819.360071.09893
1.4-1.493.90.1311.960171.08793.7
1.49-1.63.90.09114.561001.04294.6
1.6-1.763.90.07116.761551.0595
1.76-2.023.90.05120.261290.98595.6
2.02-2.544.10.05821.360750.97694.3
2.54-506.50.08318.763731.03398.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
PHENIXphasing
RefinementMethod to determine structure: Isomorphous Replacement
Starting model: PDB ID 3T4V

3t4v


Resolution: 1.18→38.77 Å / Occupancy max: 1 / Occupancy min: 0.3
RfactorNum. reflection% reflectionSelection details
Rfree0.1658 1932 3.13 %Random
Rwork0.1587 ---
obs-58383 97.2 %-
Displacement parametersBiso max: 56.85 Å2 / Biso mean: 21.6921 Å2 / Biso min: 9.29 Å2
Refinement stepCycle: LAST / Resolution: 1.18→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 23 269 1845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.0101
X-RAY DIFFRACTIONf_angle_d1.25
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.18-1.210.23341080.2231X-RAY DIFFRACTION330171
2.84-38.790.14881510.1514X-RAY DIFFRACTION457899

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