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Yorodumi- PDB-2os2: Crystal structure of JMJD2A complexed with histone H3 peptide tri... -
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-Basic information
Entry | Database: PDB / ID: 2os2 | ||||||
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Title | Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys36 | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Fe / double-stranded beta helix / demethylase / oxygenase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information [histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / response to nutrient levels / negative regulation of autophagy / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Kavanagh, K.L. / Ng, S.S. / Pilka, E. / McDonough, M.A. / Savitsky, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. ...Kavanagh, K.L. / Ng, S.S. / Pilka, E. / McDonough, M.A. / Savitsky, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Schofield, C.J. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nature / Year: 2007 Title: Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Authors: Ng, S.S. / Kavanagh, K.L. / McDonough, M.A. / Butler, D. / Pilka, E.S. / Lienard, B.M. / Bray, J.E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Rose, N.R. / Offer, J. / Scheinost, J.C. / ...Authors: Ng, S.S. / Kavanagh, K.L. / McDonough, M.A. / Butler, D. / Pilka, E.S. / Lienard, B.M. / Bray, J.E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Rose, N.R. / Offer, J. / Scheinost, J.C. / Borowski, T. / Sundstrom, M. / Schofield, C.J. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2os2.cif.gz | 164.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2os2.ent.gz | 126.3 KB | Display | PDB format |
PDBx/mmJSON format | 2os2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2os2_validation.pdf.gz | 478.9 KB | Display | wwPDB validaton report |
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Full document | 2os2_full_validation.pdf.gz | 491.9 KB | Display | |
Data in XML | 2os2_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 2os2_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/2os2 ftp://data.pdbj.org/pub/pdb/validation_reports/os/2os2 | HTTPS FTP |
-Related structure data
Related structure data | 2oq6C 2oq7SC 2ot7C 2ox0C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ZN / End label comp-ID: ZN / Refine code: 2 / Auth seq-ID: 8 - 502 / Label seq-ID: 30
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 44326.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD2A, JHDM3A, JMJD2, KIAA0677 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O75164, 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 #2: Protein/peptide | Mass: 1275.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide |
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-Non-polymers , 4 types, 216 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG 3350, 0.1 M Citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 18, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 38324 / Num. obs: 38324 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 5187 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2oq7 Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.699 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.284 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.484 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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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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