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Yorodumi- PDB-4bxf: 60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) i... -
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-Basic information
Entry | Database: PDB / ID: 4bxf | ||||||
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Title | 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 | ||||||
Components |
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Keywords | OXIDOREDUCTASE/TRANSLATION / OXIDOREDUCTASE-TRANSLATION COMPLEX / OXIDOREDUCTASE / NON-HEME / IRON-BINDING / DSBH / DIOXYGENASE / JMJC DOMAIN / RIBOSOME BIOGENESIS / NUCLEAR PROTEIN / 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 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency ...protein-L-histidine (3S)-3-hydroxylase / peptidyl-histidine dioxygenase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / histone demethylase activity / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / HDMs demethylate histones / Regulation of expression of SLITs and ROBOs / transcription corepressor activity / ribosome biogenesis / cytosolic large ribosomal subunit / cytoplasmic translation / transcription regulator complex / structural constituent of ribosome / translation / synapse / nucleolus / endoplasmic reticulum / RNA binding / nucleoplasm / membrane / identical protein binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Chowdhury, R. / 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 | 4bxf.cif.gz | 190.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bxf.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/4bxf ftp://data.pdbj.org/pub/pdb/validation_reports/bx/4bxf | HTTPS FTP |
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-Related structure data
Related structure data | 2xdvC 4bu2SC 4ccjC 4cckC 4cclC 4ccmC 4ccnC 4ccoC 4cswC 4cugC 4litC 4liuC 4livC C: citing same article (ref.) S: Starting model for refinement |
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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: 50372.215 Da / Num. of mol.: 2 / 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) 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 #2: Protein/peptide | Mass: 2279.565 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-50 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P46776 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.66 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: VAPOR DIFFUSION SITTING DROP. 0.1M BIS-TRIS PROPANE PH 8.5, 0.02M NA-K-PHOSPHATE, 20-22% (W/V) PEG 3350, 0.002 M MNCL2, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→64.83 Å / Num. obs: 64784 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BU2 Resolution: 2.05→64.83 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 298958.79 / 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: 61.7167 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→64.83 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.16 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 7
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Xplor file |
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