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- PDB-6i9l: JmjC domain-containing protein 5 (JMJD5) in complex with Mn and p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i9l | ||||||
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Title | JmjC domain-containing protein 5 (JMJD5) in complex with Mn and pyridine-2,4-dicarboxylic acid (2,4-PDCA) | ||||||
![]() | 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 / 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 ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / 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 / 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 | ![]() | 116.4 KB | Display | ![]() |
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PDB format | ![]() | 89 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6i9mC ![]() 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
#1: Protein | Mass: 29733.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8N371, [histone H3]-dimethyl-L-lysine36 demethylase, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-PD2 / |
#4: Chemical | ChemComp-TRS / |
#5: 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, 300 NL SITTING DROPS (SAMPLE:WELL, 2:1 RATIO) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2015 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91741 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→41.836 Å / Num. obs: 38444 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.52 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.052 / Rrim(I) all: 0.13 / Net I/σ(I): 17.64 |
Reflection shell | Resolution: 1.53→1.58 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 6.56 / Num. unique obs: 3781 / CC1/2: 0.898 / Rpim(I) all: 0.247 / Rrim(I) all: 0.605 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GJZ Resolution: 1.53→41.836 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→41.836 Å
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Refine LS restraints |
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LS refinement shell |
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