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- PDB-6i9m: JmjC domain-containing protein 5 (JMJD5) in complex with Mn and R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i9m | ||||||
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Title | JmjC domain-containing protein 5 (JMJD5) in complex with Mn and R-2-hydroxyglutarate | ||||||
![]() | JmjC domain-containing protein 5 | ||||||
![]() | OXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / JMJC / JMJC DOMAIN / Lysine-specific demethylase 8 / JmjC domain-containing protein 5 / Arginyl C-3 Hydroxylase / JMJD5 / KDM8 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSLATION / DSBH / FACIAL TRIAD / CYTOPLASM / JMJC HYDROXYLASE / JMJC DEMETHYLASE / KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM / BETA-HYDROXYLATION / HYDROXYLATION / ARGININE HYDROXYLATION / RCC1 domain-containing protein 1 / RCCD1 / Regulator of chromosome condensation / 40S ribosomal protein S6 / RPS6 / RIBOSOME BIOGENESIS / TRANSCRIPTION / EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / TRANSCRIPTION ACTIVATOR/INHIBITOR / PHOSPHORYLATION / CANCER / POLYMORPHISM | ||||||
Function / homology | ![]() [protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / wybutosine biosynthetic process / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / wybutosine biosynthetic process / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / tRNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chowdhury, R. / Islam, M.S. / Schofield, C.J. | ||||||
![]() | ![]() Title: Structural analysis of the 2-oxoglutarate binding site of the circadian rhythm linked oxygenase JMJD5. Authors: Islam, M.S. / Markoulides, M. / Chowdhury, R. / Schofield, C.J. #1: ![]() Title: JMJD5 is a human arginyl C-3 hydroxylase. Authors: Wilkins, S.E. / Islam, M.S. / Gannon, J.M. / Markolovic, S. / Hopkinson, R.J. / Ge, W. / Schofield, C.J. / Chowdhury, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.6 KB | Display | ![]() |
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PDB format | ![]() | 86.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 455.9 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i9lC ![]() 6i9nC ![]() 7uq3C ![]() 4gjzS S: Starting model for refinement 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29733.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CATALYTIC DOMAIN (RESIDUES 183-416) / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8N371, [histone H3]-dimethyl-L-lysine36 demethylase, Hydrolases; Acting on peptide bonds (peptidases) |
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-Non-polymers , 5 types, 199 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/2HG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/2HG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / | ||
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#3: Chemical | ChemComp-2HG / ( | ||
#4: Chemical | ChemComp-TRS / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2015 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→41.749 Å / Num. obs: 30597 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.046 / Rrim(I) all: 0.118 / Net I/σ(I): 18.17 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 3.18 / Num. unique obs: 2984 / CC1/2: 0.765 / Rpim(I) all: 0.341 / Rrim(I) all: 0.861 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GJZ Resolution: 1.65→41.749 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 51.8 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→41.749 Å
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Refine LS restraints |
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LS refinement shell |
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