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Yorodumi- PDB-4aap: Crystal structure of JMJD5 domain of human Lysine-specific demeth... -
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-Basic information
Entry | Database: PDB / ID: 4aap | ||||||
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Title | Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG) | ||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 8 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information [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 / protein destabilization / circadian regulation of gene expression ...[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 / protein destabilization / circadian regulation of gene expression / G2/M transition of mitotic cell cycle / p53 binding / chromosome / fibroblast proliferation / in utero embryonic development / endopeptidase activity / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Vollmar, M. / Johansson, C. / Krojer, T. / Canning, P. / Allerston, C. / Gadhave, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. ...Vollmar, M. / Johansson, C. / Krojer, T. / Canning, P. / Allerston, C. / Gadhave, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Jmjd5 Domain of Human Lysine- Specific Demethylase 8 (Kdm8) in Complex with N- Oxalylglycine (Nog) Authors: Vollmar, M. / Johansson, C. / Krojer, T. / Canning, P. / Allerston, C. / Gadhave, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aap.cif.gz | 201.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aap.ent.gz | 162.3 KB | Display | PDB format |
PDBx/mmJSON format | 4aap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aap_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
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Full document | 4aap_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 4aap_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 4aap_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/4aap ftp://data.pdbj.org/pub/pdb/validation_reports/aa/4aap | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27764.521 Da / Num. of mol.: 2 / Fragment: JMJD5 DOMAIN, RESIDUES 218-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: Q8N371, [histone H3]-dimethyl-L-lysine36 demethylase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 3.3 Å3/Da / Density % sol: 62.73 % / Description: NONE |
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Crystal grow | Details: 16% PEG_3350, 0.007M NICL, 0M CDCL, 0.007M MGCL, 0.1M HEPES PH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.91 Å / Num. obs: 23473 / % possible obs: 99.5 % / Observed criterion σ(I): 2.2 / Redundancy: 7 % / Biso Wilson estimate: 88.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.6→89.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.432 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: 65.507 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→89.67 Å
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