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Open data
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Basic information
Entry | Database: PDB / ID: 2xdv | ||||||
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Title | Crystal Structure of the Catalytic Domain of FLJ14393 | ||||||
![]() | MYC-INDUCED NUCLEAR ANTIGEN | ||||||
![]() | NUCLEAR PROTEIN / RIBOSOME BIOGENESIS | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Krojer, T. / Muniz, J.R.C. / Ng, S.S. / Pilka, E. / Guo, K. / Pike, A.C.W. / Filippakopoulos, P. / Knapp, S. / Kavanagh, K.L. / Gileadi, O. ...Krojer, T. / Muniz, J.R.C. / Ng, S.S. / Pilka, E. / Guo, K. / Pike, A.C.W. / Filippakopoulos, P. / Knapp, S. / Kavanagh, K.L. / Gileadi, O. / Bunkoczi, G. / Yue, W.W. / Niesen, F. / Sobott, F. / Fedorov, O. / Savitsky, P. / Kochan, G. / Daniel, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.5 KB | Display | ![]() |
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PDB format | ![]() | 140.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
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Full document | ![]() | 454.8 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bu2C ![]() 4bxfC ![]() 4ccjC ![]() 4cckC ![]() 4cclC ![]() 4ccmC ![]() 4ccnC ![]() 4ccoC ![]() 4cswC ![]() 4cugC ![]() 4litC ![]() 4liuC ![]() 4livC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50462.270 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 26-465 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 161 molecules ![](data/chem/img/OGA.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-OGA / | ||||||||
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#3: Chemical | ChemComp-NI / #4: Chemical | ChemComp-MN / | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.35 Å3/Da / Density % sol: 77 % / Description: NONE |
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Crystal grow | Details: 12% PEG 3350; 0.005M COCL2; 0.005M MGCL2; 0.005M CDCL2; 0.005M NICL2; 0.1M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→30 Å / Num. obs: 35135 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 68.36 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.56→2.7 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.57→29.28 Å / Cor.coef. Fo:Fc: 0.9384 / Cor.coef. Fo:Fc free: 0.9239 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NI MN OGA CD. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3205. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NI MN OGA CD. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3205. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=10. NUMBER TREATED BY BAD NON- BONDED CONTACTS=10
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Displacement parameters | Biso mean: 65.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.57→29.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.57→2.64 Å / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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