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Open data
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Basic information
Entry | Database: PDB / ID: 4gjy | ||||||
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Title | JMJD5 in complex with N-Oxalylglycine | ||||||
![]() | JmjC domain-containing protein 5 | ||||||
![]() | OXIDOREDUCTASE / JmjC / beta barrel / Fe(II) and 2-oxoglutarate binding | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Del Rizzo, P.A. / Trievel, R.C. | ||||||
![]() | ![]() Title: Crystal Structure and Functional Analysis of JMJD5 Indicate an Alternate Specificity and Function. Authors: Del Rizzo, P.A. / Krishnan, S. / Trievel, R.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.5 KB | Display | ![]() |
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PDB format | ![]() | 128.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.7 KB | Display | ![]() |
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Full document | ![]() | 431.7 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 27402.559 Da / Num. of mol.: 1 / Fragment: JmjC Domain (UNP Residues 183-416) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8N371, [histone H3]-dimethyl-L-lysine36 demethylase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-OGA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 4.5% PEG 3000, 0.1 M Bis-Tris pH 5.5, 0.05 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 3, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 13.1 % / Av σ(I) over netI: 49.62 / Number: 892588 / Rmerge(I) obs: 0.073 / Χ2: 1.65 / D res high: 1.25 Å / D res low: 50 Å / Num. obs: 68062 / % possible obs: 98.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.249→50 Å / Num. obs: 68062 / % possible obs: 98.8 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.073 / Χ2: 1.648 / Net I/σ(I): 10.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.28 / FOM acentric: 0.29 / FOM centric: 0.23 / Reflection: 8389 / Reflection acentric: 7049 / Reflection centric: 1340 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.432 Å2 / ksol: 0.335 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.91 Å2 / Biso mean: 14.2802 Å2 / Biso min: 4.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2492→30.43 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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