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Yorodumi- PDB-4fwe: Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fwe | ||||||
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Title | Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A | ||||||
Components | Lysine-specific histone demethylase 1B | ||||||
Keywords | OXIDOREDUCTASE / lsd2 / fad / histone demethylase / C4H2C2 / CW / epigenetic | ||||||
Function / homology | Function and homology information epigenetic programing of female pronucleus / genomic imprinting / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / FAD binding / transcription initiation-coupled chromatin remodeling / HDMs demethylate histones / UCH proteinases ...epigenetic programing of female pronucleus / genomic imprinting / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / FAD binding / transcription initiation-coupled chromatin remodeling / HDMs demethylate histones / UCH proteinases / nucleosome / flavin adenine dinucleotide binding / histone binding / oxidoreductase activity / chromatin remodeling / chromatin binding / chromatin / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Zhang, Q. / Chen, Z. | ||||||
Citation | Journal: Cell Res. / Year: 2013 Title: Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b Authors: Zhang, Q. / Qi, S. / Xu, M. / Yu, L. / Tao, Y. / Deng, Z. / Wu, W. / Li, J. / Chen, Z. / Wong, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fwe.cif.gz | 171 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fwe.ent.gz | 129.6 KB | Display | PDB format |
PDBx/mmJSON format | 4fwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fwe_validation.pdf.gz | 730.4 KB | Display | wwPDB validaton report |
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Full document | 4fwe_full_validation.pdf.gz | 744.4 KB | Display | |
Data in XML | 4fwe_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 4fwe_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/4fwe ftp://data.pdbj.org/pub/pdb/validation_reports/fw/4fwe | HTTPS FTP |
-Related structure data
Related structure data | 4fwfC 4fwjSC 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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-Components
#1: Protein | Mass: 89340.977 Da / Num. of mol.: 1 / Fragment: UNP residues 30-822 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LSD2 / Plasmid: pet-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NB78, Oxidoreductases | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-FLC / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.68 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 7 Details: 21% PEG3350, 200mM diammonium citrate, pH 7, EVAPORATION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.97943 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97943 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→50 Å / Num. all: 47400 / Num. obs: 44518 / % possible obs: 93.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.2 % |
Reflection shell | Resolution: 2.13→2.17 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1987 / Rsym value: 0.663 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FWJ Resolution: 2.13→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.254 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.269 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 49.419 Å2
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Refinement step | Cycle: LAST / Resolution: 2.13→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.185 Å / Total num. of bins used: 20
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