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- PDB-4ypa: ASH1L SET domain Q2265A mutant in complex with S-adenosyl methion... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ypa | ||||||||||||||||||||||||
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Title | ASH1L SET domain Q2265A mutant in complex with S-adenosyl methionine (SAM) | ||||||||||||||||||||||||
![]() | Histone-lysine N-methyltransferase ASH1L | ||||||||||||||||||||||||
![]() | TRANSFERASE / histone methylation / SET domain | ||||||||||||||||||||||||
Function / homology | ![]() uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / uterus morphogenesis / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / flagellated sperm motility ...uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / uterus morphogenesis / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / flagellated sperm motility / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / histone H3 methyltransferase activity / negative regulation of MAPK cascade / negative regulation of acute inflammatory response / decidualization / single fertilization / bicellular tight junction / post-embryonic development / skeletal system development / PKMTs methylate histone lysines / MAPK cascade / chromosome / methylation / transcription by RNA polymerase II / inflammatory response / chromatin binding / regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Rogawski, D.S. / Ndoj, J. / Cho, H.J. / Maillard, I. / Grembecka, J. / Cierpicki, T. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Two Loops Undergoing Concerted Dynamics Regulate the Activity of the ASH1L Histone Methyltransferase. Authors: Rogawski, D.S. / Ndoj, J. / Cho, H.J. / Maillard, I. / Grembecka, J. / Cierpicki, T. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.3 KB | Display | ![]() |
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PDB format | ![]() | 153.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 53 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ynmSC ![]() 4ynpC ![]() 4ypeC ![]() 4ypuC S: Starting model for refinement C: citing same article ( |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 25959.465 Da / Num. of mol.: 4 / Fragment: SET domain (UNP residues 2074-2293) / Mutation: Q2265A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NR48, histone-lysine N-methyltransferase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SAM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.34 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, magnesium chloride, Tris / PH range: 8.3-8.7 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 40091 / % possible obs: 96 % / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Χ2: 1.251 / Net I/av σ(I): 15.471 / Net I/σ(I): 8.1 / Num. measured all: 79637 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2 % / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YNM Resolution: 2.3→73.04 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.868 / SU B: 9.634 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.528 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.29 Å2 / Biso mean: 38.039 Å2 / Biso min: 10.3 Å2
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Refinement step | Cycle: final / Resolution: 2.3→73.04 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Number: 1712 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.296→2.356 Å / Total num. of bins used: 20
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