[English] 日本語
![](img/lk-miru.gif)
- PDB-4bu2: 60S ribosomal protein L27A histidine hydroxylase (MINA53) in comp... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4bu2 | ||||||
---|---|---|---|---|---|---|---|
Title | 60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG) | ||||||
![]() | BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA | ||||||
![]() | 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 | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chowdhury, R. / Clifton, I.J. / McDonough, M.A. / Ng, S.S. / Pilka, E. / Oppermann, U. / Schofield, C.J. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 92.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 72.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 469.5 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xdvC ![]() 4bxfC ![]() 4ccjC ![]() 4cckC ![]() 4cclC ![]() 4ccmC ![]() 4ccnC ![]() 4ccoC ![]() 4cswC ![]() 4cugC ![]() 4litC ![]() 4liuC ![]() 4livC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() 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: Chemical | #3: Chemical | ChemComp-AKG / | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.14 Å3/Da / Density % sol: 76.1 % / Description: NONE |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.0245 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.78→37.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|