Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Ribosomal oxygenases are structurally conserved from prokaryotes to humans.
Journal, issue, pages	Nature, Vol. 510, Page 422-426, Year 2014
Publish date	May 7, 2010 (structure data deposition date)
Authors	Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. ...Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E.S. / Kavanagh, K.L. / von Delft, F. / Oppermann, U. / McDonough, M.A. / Doherty, A.J. / Schofield, C.J.
External links	Nature / PubMed:24814345
Methods	X-ray diffraction
Resolution	2.05 - 2.96 Å
Structure data	PDB-2xdv: Crystal Structure of the Catalytic Domain of FLJ14393 Method: X-RAY DIFFRACTION / Resolution: 2.57 Å PDB-4bu2: 60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG) Method: X-RAY DIFFRACTION / Resolution: 2.78 Å PDB-4bxf: 60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment Method: X-RAY DIFFRACTION / Resolution: 2.05 Å PDB-4ccj: 60S ribosomal protein L8 histidine hydroxylase (NO66) in apo form Method: X-RAY DIFFRACTION / Resolution: 2.15 Å PDB-4cck: 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II) and N-oxalylglycine (NOG) Method: X-RAY DIFFRACTION / Resolution: 2.15 Å PDB-4ccl: X-Ray structure of E. coli ycfD Method: X-RAY DIFFRACTION / Resolution: 2.596 Å PDB-4ccm: 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1) Method: X-RAY DIFFRACTION / Resolution: 2.51 Å PDB-4ccn: 60S ribosomal protein L8 histidine hydroxylase (NO66 L299C/C300S) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-2) Method: X-RAY DIFFRACTION / Resolution: 2.23 Å PDB-4cco: 60S ribosomal protein L8 histidine hydroxylase (NO66 S373C) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G214C) peptide fragment (complex-3) Method: X-RAY DIFFRACTION / Resolution: 2.3 Å PDB-4csw: Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase Method: X-RAY DIFFRACTION / Resolution: 2.821 Å PDB-4cug: Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase in complex substrate fragment Method: X-RAY DIFFRACTION / Resolution: 2.96 Å PDB-4lit: Structure of YcfD a Ribosomal oxygenase from Escherichia coli in complex with Cobalt and 2-oxoglutarate. Method: X-RAY DIFFRACTION / Resolution: 2.4 Å PDB-4liu: Structure of YcfD, a Ribosomal oxygenase from Escherichia coli. Method: X-RAY DIFFRACTION / Resolution: 2.7 Å PDB-4liv: Structure of YcfD, a Ribosomal oxygenase from Escherichia coli in complex with Cobalt and succinic acid. Method: X-RAY DIFFRACTION / Resolution: 2.7 Å
Chemicals	ChemComp-OGA: N-OXALYLGLYCINE / inhibitorYM ChemComp-NI: NICKEL (II) ION ChemComp-MN: Unknown entry ChemComp-EDO: 1,2-ETHANEDIOL ChemComp-CD: Unknown entry ChemComp-HOH: WATER ChemComp-AKG: 2-OXOGLUTARIC ACID ChemComp-SO4: SULFATE ION ChemComp-CIT: CITRIC ACID ChemComp-UN9: N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE ChemComp-GOL: GLYCEROL ChemComp-MPD: (4S)-2-METHYL-2,4-PENTANEDIOL / precipitantYM ChemComp-PO4: PHOSPHATE ION ChemComp-CO: Unknown entry ChemComp-TAM: TRIS(HYDROXYETHYL)AMINOMETHANE / pH bufferYM ChemComp-SIN*: SUCCINIC ACID
Source	homo sapiens (human) escherichia coli (E. coli) rhodothermus marinus (bacteria)
Keywords	NUCLEAR PROTEIN / RIBOSOME BIOGENESIS / OXIDOREDUCTASE / NON-HEME / IRON-BINDING / DSBH / 2-OXOGLUTARATE / DIOXYGENASE / JMJC DOMAIN / RPL27A / BETA-HYDROXYLATION / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING / OXIDOREDUCTASE/TRANSLATION / OXIDOREDUCTASE-TRANSLATION COMPLEX / RPL8 / 2OG AND IRON DEPENDENT OXYGENASE / 2- OXOGLUTARATE / 2-OXOGLUTARATE AND IRON DEPENDENT OXYGENASE / DOUBLE STRANDED BETA HELIX FOLD / TRANSLATION / Hydroxylation