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Yorodumi- PDB-4bu2: 60S ribosomal protein L27A histidine hydroxylase (MINA53) in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bu2 | ||||||
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Title | 60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG) | ||||||
Components | BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA | ||||||
Keywords | OXIDOREDUCTASE / NON-HEME / IRON-BINDING / DSBH / 2-OXOGLUTARATE / DIOXYGENASE / JMJC DOMAIN / RIBOSOME BIOGENESIS / NUCLEAR PROTEIN / RPL27A / BETA-HYDROXYLATION / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING | ||||||
Function / homology | Function and homology information protein-L-histidine (3S)-3-hydroxylase / peptidyl-histidine dioxygenase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / Protein hydroxylation / histone demethylase activity / HDMs demethylate histones / transcription corepressor activity / ribosome biogenesis / transcription regulator complex ...protein-L-histidine (3S)-3-hydroxylase / peptidyl-histidine dioxygenase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / Protein hydroxylation / histone demethylase activity / HDMs demethylate histones / transcription corepressor activity / ribosome biogenesis / transcription regulator complex / nucleolus / nucleoplasm / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.78 Å | ||||||
Authors | Chowdhury, R. / Clifton, I.J. / McDonough, M.A. / Ng, S.S. / Pilka, E. / Oppermann, U. / Schofield, C.J. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Ribosomal oxygenases are structurally conserved from prokaryotes to humans. 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. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E. ...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. / 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. #1: Journal: Nat.Chem.Biol. / Year: 2012 Title: Oxygenase-Catalyzed Ribosome Hydroxylation Occurs in Prokaryotes and Humans. Authors: Ge, W. / Wolf, A. / Feng, T. / Ho, C. / Sekirnik, R. / Zayer, A. / Granatino, N. / Cockman, M.E. / Loenarz, C. / Loik, N.D. / Hardy, A.P. / Claridge, T.D.W. / Hamed, R.B. / Chowdhury, R. / ...Authors: Ge, W. / Wolf, A. / Feng, T. / Ho, C. / Sekirnik, R. / Zayer, A. / Granatino, N. / Cockman, M.E. / Loenarz, C. / Loik, N.D. / Hardy, A.P. / Claridge, T.D.W. / Hamed, R.B. / Chowdhury, R. / Gong, L. / Robinson, C.V. / Trudgian, D.C. / Jiang, M. / Mackeen, M.M. / Mccullagh, J.S. / Gordiyenko, Y. / Thalhammer, A. / Yamamoto, A. / Yang, M. / Liu-Yi, P. / Zhang, Z. / Schmidt-Zachmann, M. / Kessler, B.M. / Ratcliffe, P.J. / Preston, G.M. / Coleman, M.L. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bu2.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bu2.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/4bu2 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/4bu2 | HTTPS FTP |
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-Related structure data
Related structure data | 2xdvC 4bxfC 4ccjC 4cckC 4cclC 4ccmC 4ccnC 4ccoC 4cswC 4cugC 4litC 4liuC 4livC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50837.426 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 26-465 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q8IUF8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor | ||||||
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#2: Chemical | #3: Chemical | ChemComp-AKG / | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.14 Å3/Da / Density % sol: 76.1 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M BIS-TRIS PROPANE PH 6.5, 19-22% (W/V) PEG 3350, 0.2M AMMONIUM SULPHATE, 0.005M NICL2, TEMPERATURE 293K. VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9699 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→37.69 Å / Num. obs: 27690 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 40.7 % / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.78→2.93 Å / Redundancy: 42 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.78→37.69 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 115409.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.0245 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.78→37.69 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.78→2.93 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 7
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Xplor file |
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