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Yorodumi- PDB-1hdd: CRYSTAL STRUCTURE OF AN ENGRAILED HOMEODOMAIN-DNA COMPLEX AT 2.8 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hdd | ||||||
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Title | CRYSTAL STRUCTURE OF AN ENGRAILED HOMEODOMAIN-DNA COMPLEX AT 2.8 ANGSTROMS RESOLUTION: A FRAMEWORK FOR UNDERSTANDING HOMEODOMAIN-DNA INTERACTIONS | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-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 / DNA-binding transcription repressor activity, RNA polymerase II-specific / neuron differentiation / regulation of gene expression / sequence-specific DNA binding / negative regulation of neuron apoptotic process / 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 / Resolution: 2.8 Å | ||||||
Authors | Kissinger, C.R. / Liu, B. / Martin-Blanco, E. / Kornberg, T.B. / Pabo, C.O. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1990 Title: Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. Authors: Kissinger, C.R. / Liu, B.S. / Martin-Blanco, E. / Kornberg, T.B. / Pabo, C.O. #1: Journal: Biochem.Biophys.Res.Commun. / Year: 1990 Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Engrailed Homeodomain and of an Engrailed Homeodomain Complex Authors: Liu, B. / Kissinger, C.R. / Pabo, C.O. / Martin-Blanco, E. / Kornberg, T.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hdd.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hdd.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 1hdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hdd_validation.pdf.gz | 383.2 KB | Display | wwPDB validaton report |
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Full document | 1hdd_full_validation.pdf.gz | 405.8 KB | Display | |
Data in XML | 1hdd_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1hdd_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/1hdd ftp://data.pdbj.org/pub/pdb/validation_reports/hd/1hdd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6387.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 6494.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 7469.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P02836 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.48 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.7 / Details: pH 6.70, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: unknown / PH range low: 9 / PH range high: 8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.8 Å / Num. obs: 9072 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 21130 / Rmerge(I) obs: 0.0426 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.8→10.001 Å /
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Refinement step | Cycle: LAST / Resolution: 2.8→10.001 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Rfactor obs: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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