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Open data
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Basic information
Entry | Database: PDB / ID: 4ij8 | ||||||
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Title | Crystal structure of the complex of SETD8 with SAM | ||||||
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Function / homology | ![]() histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / peptidyl-lysine monomethylation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() unidentified (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Yu, W. / Tempel, W. / Li, Y. / El Bakkouri, M. / Shapira, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Crystal structure of the complex of SETD8 with SAM Authors: Yu, W. / Tempel, W. / Li, Y. / El Bakkouri, M. / Shapira, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.3 KB | Display | ![]() |
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PDB format | ![]() | 112 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1zkkS 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18717.139 Da / Num. of mol.: 2 / Mutation: C343S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9NQR1, ![]() ![]() #2: Protein/peptide | | Mass: 869.063 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: ![]() ![]() ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-UNX / #5: Water | ChemComp-HOH / | ![]() Sequence details | THE MODEL INCLUDES A DISJOINT APPARENT ALPHA-HELIX THAT COULD NOT BE ASSIGNED TO A SPECIFIC SECTION ...THE MODEL INCLUDES A DISJOINT APPARENT ALPHA-HELIX THAT COULD NOT BE ASSIGNED TO A SPECIFIC SECTION OF THE AMINO ACID SEQUENCE OF THE TARGET PROTEIN. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.94 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 1.2 M sodium citrate, 0.1 M HEPES, 10-fold excess SAM, pH 7.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 25, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→87.849 Å / Num. all: 29619 / Num. obs: 29619 / % possible obs: 100 % / Redundancy: 21.6 % / Rsym value: 0.112 / Net I/σ(I): 19.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1ZKK Resolution: 2→43.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1892 / WRfactor Rwork: 0.1704 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8803 / SU B: 6.332 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1405 / SU Rfree: 0.1248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED ARP/WARP, COOT, AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT.
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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 max: 97.23 Å2 / Biso mean: 37.7619 Å2 / Biso min: 15.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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