+Open data
-Basic information
Entry | Database: PDB / ID: 5fzo | ||||||
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Title | Crystal structure of the catalytic domain of human JmjD1C | ||||||
Components | (PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / JMJD1C | ||||||
Function / homology | Function and homology information 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 / nuclear thyroid hormone receptor binding / dioxygenase activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / chromatin ...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 / nuclear thyroid hormone receptor binding / dioxygenase activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Nowak, R. / Talon, R. / Krojer, T. / Goubin, S. / McDonough, M. / Fairhead, M. / Oppermann, U. / Johansson, C. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Catalytic Domain of Human Jmjd1C Authors: Nowak, R. / Goubin, S. / Mcdonough, M. / Fairhead, M. / Oppermann, U. / Johansson, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fzo.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fzo.ent.gz | 128.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/5fzo ftp://data.pdbj.org/pub/pdb/validation_reports/fz/5fzo | HTTPS FTP |
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-Related structure data
Related structure data | 2ypdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN ... , 2 types, 2 molecules AB
#1: Protein | Mass: 40373.176 Da / Num. of mol.: 1 / Fragment: JUMONJI DOMAIN, UNP RESIDUES 2157-2500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q15652, 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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#2: Protein | Mass: 40401.184 Da / Num. of mol.: 1 / Fragment: JUMONJI DOMAIN, UNP RESIDUES 2157-2500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q15652, 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 |
-Non-polymers , 4 types, 509 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | M COME FROM THE EXPRESSION |
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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: 2.69 Å3/Da / Density % sol: 54.26 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 20% PEG3350 -- 10% ETHYLENE GLYCOL -- 0.1M BIS-TRIS-PROPANE PH 8.5 -- 0.2M POTASSIUM CITRATE TRIBASIC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96859 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→55.46 Å / Num. obs: 72743 / % possible obs: 99.1 % / Observed criterion σ(I): 1.1 / Redundancy: 6.6 % / Biso Wilson estimate: 28.84 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.84→1.89 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.1 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YPD Resolution: 1.84→55.46 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 25.24 / Stereochemistry target values: ML Details: CYSTEINE 2317 IN CHAIN A AND B IS MODIFIED TO SULFENIC ACID (CSD).
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→55.46 Å
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Refine LS restraints |
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LS refinement shell |
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