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Yorodumi- PDB-4ccj: 60S ribosomal protein L8 histidine hydroxylase (NO66) in apo form -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ccj | ||||||
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Title | 60S ribosomal protein L8 histidine hydroxylase (NO66) in apo form | ||||||
Components | BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66 | ||||||
Keywords | OXIDOREDUCTASE / NON-HEME / IRON-BINDING / DSBH / DIOXYGENASE / JMJC DOMAIN / RIBOSOME BIOGENESIS / NUCLEAR PROTEIN / RPL8 / BETA-HYDROXYLATION / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING | ||||||
Function / homology | Function and homology information protein-L-histidine (3S)-3-hydroxylase / protein demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / peptidyl-histidine dioxygenase activity / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / negative regulation of osteoblast differentiation ...protein-L-histidine (3S)-3-hydroxylase / protein demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / peptidyl-histidine dioxygenase activity / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / negative regulation of osteoblast differentiation / Protein hydroxylation / iron ion binding / negative regulation of DNA-templated transcription / nucleolus / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Chowdhury, R. / Ge, W. / Clifton, I.J. / 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 | 4ccj.cif.gz | 387.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ccj.ent.gz | 317 KB | Display | PDB format |
PDBx/mmJSON format | 4ccj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ccj_validation.pdf.gz | 470.5 KB | Display | wwPDB validaton report |
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Full document | 4ccj_full_validation.pdf.gz | 502.2 KB | Display | |
Data in XML | 4ccj_validation.xml.gz | 75.8 KB | Display | |
Data in CIF | 4ccj_validation.cif.gz | 106.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/4ccj ftp://data.pdbj.org/pub/pdb/validation_reports/cc/4ccj | HTTPS FTP |
-Related structure data
Related structure data | 2xdvC 4bu2C 4bxfC 4cckC 4cclC 4ccmC 4ccnC 4ccoC 4cswC 4cugC 4litC 4liuC 4livC 4diqS 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: 53241.191 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 183-641 / 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: Q9H6W3, 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 ...References: UniProt: Q9H6W3, 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, [histone H3]-dimethyl-L-lysine36 demethylase #2: Chemical | #3: 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: 3.04 Å3/Da / Density % sol: 59.6 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: NAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 5.6-6.5, 0.5-0.7M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 7, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→63.72 Å / Num. obs: 128285 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.3 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4DIQ Resolution: 2.15→63.72 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 130909.27 / 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: 58.6314 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→63.72 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.21 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 12
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Xplor file |
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