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Yorodumi- PDB-7m98: ATAD2 bromodomain complexed with histone H4K5ac (res 1-10) ligand -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m98 | |||||||||
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Title | ATAD2 bromodomain complexed with histone H4K5ac (res 1-10) ligand | |||||||||
Components |
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Keywords | NUCLEAR PROTEIN / Bromodomain / epigenetics | |||||||||
Function / homology | Function and homology information nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process ...nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Malone, K.L. / Phillips, M. / Nix, J.C. / Glass, K.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Int J Mol Sci / Year: 2021 Title: Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain. Authors: Evans, C.M. / Phillips, M. / Malone, K.L. / Tonelli, M. / Cornilescu, G. / Cornilescu, C. / Holton, S.J. / Gorjanacz, M. / Wang, L. / Carlson, S. / Gay, J.C. / Nix, J.C. / Demeler, B. / ...Authors: Evans, C.M. / Phillips, M. / Malone, K.L. / Tonelli, M. / Cornilescu, G. / Cornilescu, C. / Holton, S.J. / Gorjanacz, M. / Wang, L. / Carlson, S. / Gay, J.C. / Nix, J.C. / Demeler, B. / Markley, J.L. / Glass, K.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m98.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m98.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 7m98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m98_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 7m98_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 7m98_validation.xml.gz | 10 KB | Display | |
Data in CIF | 7m98_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/7m98 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/7m98 | HTTPS FTP |
-Related structure data
Related structure data | 4tt2S 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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Unit cell |
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-Components
#1: Protein | Mass: 17858.201 Da / Num. of mol.: 1 / Mutation: C1101A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q6PL18, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: Protein/peptide | Mass: 1331.505 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4 Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P62805 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 2.0 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 6.6 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Dec 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→44.54 Å / Num. obs: 32508 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 26.92 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.0178 / Rrim(I) all: 0.136 / Net I/σ(I): 18.87 |
Reflection shell | Resolution: 1.59→1.62 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6612 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 3090 / CC1/2: 0.495 / CC star: 0.814 / Rpim(I) all: 0.6612 / Rrim(I) all: 0.935 / % possible all: 97.14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TT2 Resolution: 1.6→44.54 Å / SU ML: 0.195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0029 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→44.54 Å
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Refine LS restraints |
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LS refinement shell |
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