+Open data
-Basic information
Entry | Database: PDB / ID: 3ld8 | ||||||
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Title | Structure of JMJD6 and Fab Fragments | ||||||
Components |
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Keywords | IMMUNE SYSTEM / JMJD6 / Fab Fragments | ||||||
Function / homology | Function and homology information peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine / histone H3R2 demethylase activity / peptidyl-lysine 5-dioxygenase activity / histone H4R3 demethylase activity / protein demethylase activity / recognition of apoptotic cell / negative regulation of protein homooligomerization / oxidative RNA demethylation / oxidative RNA demethylase activity / 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 ...peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine / histone H3R2 demethylase activity / peptidyl-lysine 5-dioxygenase activity / histone H4R3 demethylase activity / protein demethylase activity / recognition of apoptotic cell / negative regulation of protein homooligomerization / oxidative RNA demethylation / oxidative RNA demethylase activity / 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 / macrophage activation / non-membrane-bounded organelle assembly / transcription regulator activator activity / regulation of mRNA splicing, via spliceosome / sprouting angiogenesis / Protein hydroxylation / erythrocyte development / P-TEFb complex binding / histone demethylase activity / phagocytosis / RNA splicing / kidney development / lung development / protein homooligomerization / HDMs demethylate histones / mRNA processing / retina development in camera-type eye / signaling receptor activity / heart development / T cell differentiation in thymus / single-stranded RNA binding / cell surface receptor signaling pathway / chromatin remodeling / ribonucleoprotein complex / iron ion binding / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Cricetulus migratorius (Armenian hamster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Hong, X. / Zang, J. / White, J. / Kappler, J.W. / Wang, C. / Zhang, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Interaction of JMJD6 with single-stranded RNA. Authors: Hong, X. / Zang, J. / White, J. / Wang, C. / Pan, C.H. / Zhao, R. / Murphy, R.C. / Dai, S. / Henson, P. / Kappler, J.W. / Hagman, J. / Zhang, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ld8.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ld8.ent.gz | 134.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ld8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/3ld8 ftp://data.pdbj.org/pub/pdb/validation_reports/ld/3ld8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39437.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD6, JMJD6(1-403), KIAA0585, PTDSR / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q6NYC1, 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 |
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-Antibody , 2 types, 2 molecules BC
#2: Antibody | Mass: 24100.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus migratorius (Armenian hamster) Cell: hybridoma / Production host: Cricetulus migratorius (Armenian hamster) |
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#3: Antibody | Mass: 24007.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus migratorius (Armenian hamster) Cell: hybridoma / Production host: Cricetulus migratorius (Armenian hamster) |
-Non-polymers , 4 types, 27 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-FE / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 5.01 Å3/Da / Density % sol: 75.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M Bis(2-hydroxyethyl)-amino-tris(hydroxymethyl)-methane, 2.1M Ammonium Sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.61→99 Å / Num. all: 54610 / Num. obs: 40942 / % possible obs: 75 % / Biso Wilson estimate: 40.7 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→48.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 66781.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.9594 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→48.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
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Xplor file |
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