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- PDB-4igq: Histone H3 Lysine 4 Demethylating Rice JMJ703 in complex with met... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4igq | ||||||
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Title | Histone H3 Lysine 4 Demethylating Rice JMJ703 in complex with methylated H3K4 substrate | ||||||
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![]() | STRUCTURAL PROTEIN/TRANSCRIPTION / JumonjiC / Histone demethylase / STRUCTURAL PROTEIN-TRANSCRIPTION complex | ||||||
Function / homology | ![]() positive regulation of growth rate / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K4 demethylase activity / negative regulation of gene expression, epigenetic / ferrous iron binding / regulation of gene expression / chromatin remodeling / chromatin / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Q.F. / Chen, X.S. / Wang, Q. / Zhang, F.B. / Lou, Z.Y. / Zhang, Q.F. / Zhou, D.X. | ||||||
![]() | ![]() Title: Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice. Authors: Chen, Q. / Chen, X. / Wang, Q. / Zhang, F. / Lou, Z. / Zhang, Q. / Zhou, D.X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.1 KB | Display | ![]() |
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PDB format | ![]() | 55.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
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Full document | ![]() | 467.1 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4igoC ![]() 4igpC ![]() 2oq6S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 40968.012 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 139-459 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: P0617H07.8, Os05g0196500 / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 418.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis |
#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-OGA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: potassium phosphate monobasic, 25% (w/v) polyethylene glycol 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 15151 / Num. obs: 15108 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OQ6 Resolution: 2.35→39.588 Å / SU ML: 0.55 / σ(F): 0.87 / Phase error: 22.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.804 Å2 / ksol: 0.327 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.35→39.588 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %
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