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Open data
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Basic information
Entry | Database: PDB / ID: 6chg | ||||||
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Title | Crystal structure of the yeast COMPASS catalytic module | ||||||
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![]() | TRANSFERASE / Histones / S-adenosylmethionine / Complex / enzyme | ||||||
Function / homology | ![]() [histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / chromosome / histone binding / methylation / transcription cis-regulatory region binding / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsu, P.L. / Li, H. / Zheng, N. | ||||||
![]() | ![]() Title: Crystal Structure of the COMPASS H3K4 Methyltransferase Catalytic Module. Authors: Hsu, P.L. / Li, H. / Lau, H.T. / Leonen, C. / Dhall, A. / Ong, S.E. / Chatterjee, C. / Zheng, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 507.8 KB | Display | ![]() |
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PDB format | ![]() | 416 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 829.7 KB | Display | ![]() |
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Full document | ![]() | 848.5 KB | Display | |
Data in XML | ![]() | 46.6 KB | Display | |
Data in CIF | ![]() | 63 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-Protein , 5 types, 6 molecules ABCDEF
#1: Protein | Mass: 34793.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_E24487g / Production host: ![]() |
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#2: Protein | Mass: 47286.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_C10945g / Production host: ![]() |
#3: Protein | Mass: 17420.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: SET1, KLLA0F24134g / Production host: ![]() References: UniProt: Q6CIT4, histone-lysine N-methyltransferase |
#4: Protein | Mass: 49894.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_A08800g / Production host: ![]() |
#5: Protein | Mass: 6900.937 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_E03521g / Production host: ![]() |
-Protein/peptide , 1 types, 1 molecules J
#6: Protein/peptide | Mass: 535.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 12 molecules ![](data/chem/img/SAM.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-SAM / |
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#8: Chemical | ChemComp-ZN / |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.34 Å3/Da / Density % sol: 71.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Sodium Tartrate, PEG20000, ATP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.985→50 Å / Num. obs: 54818 / % possible obs: 96.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.063 / Rrim(I) all: 0.165 / Net I/σ(I): 14.73 |
Reflection shell | Resolution: 2.985→3.05 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.175 / Num. unique obs: 2416 / CC1/2: 0.569 / Rpim(I) all: 0.474 / % possible all: 86.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5F6K, 2H14 Resolution: 2.985→44.607 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.61 / Stereochemistry target values: ML
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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: 2.985→44.607 Å
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Refine LS restraints |
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LS refinement shell |
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