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Yorodumi- PDB-6m3d: X-ray crystal structure of tandemly connected engrailed homeodoma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m3d | ||||||||||||
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Title | X-ray crystal structure of tandemly connected engrailed homeodomains (EHD) with R53A mutations and DNA complex | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / HOMEODOMAIN FOLD / PROTEIN-DNA COMPLEX / GENOME EDITING / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation ...posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / wing disc morphogenesis / neuroblast fate determination / imaginal disc-derived wing vein specification / segment polarity determination / ventral midline development / compartment pattern specification / gonad development / axon guidance / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / negative regulation of neuron apoptotic process / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||||||||
Biological species | Drosophila melanogaster (fruit fly) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Sunami, T. / Hirano, Y. / Tamada, T. / Kono, H. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structural basis for designing an array of engrailed homeodomains. Authors: Sunami, T. / Hirano, Y. / Tamada, T. / Kono, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m3d.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m3d.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 6m3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/6m3d ftp://data.pdbj.org/pub/pdb/validation_reports/m3/6m3d | HTTPS FTP |
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-Related structure data
Related structure data | 2hddS 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: DNA chain | Mass: 3581.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3741.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 17344.592 Da / Num. of mol.: 1 / Mutation: Q503K,R506A Source method: isolated from a genetically manipulated source Details: the fusion protein of EHD (UNP RESIDUES 453-512), linkers GGGGG, EHD (UNP RESIDUES 453-512) Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: en, CG9015 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02836 |
#4: Chemical | ChemComp-NA / |
#5: 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: 1.9 Å3/Da / Density % sol: 35.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 8% (w/v) PEG 4000, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38.17 Å / Num. obs: 24423 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.1623401697 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.025 / Rrim(I) all: 0.034 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1183 / CC1/2: 0.921 / Rrim(I) all: 0.338 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HDD Resolution: 1.6→38.17 Å / SU ML: 0.174027637387 / Cross valid method: FREE R-VALUE / σ(F): 1.40888796396 / Phase error: 23.6012510998 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: 26.5017300563 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→38.17 Å
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Refine LS restraints |
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LS refinement shell |
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