+Open data
-Basic information
Entry | Database: PDB / ID: 3hdd | ||||||
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Title | ENGRAILED HOMEODOMAIN DNA COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / DNA BINDING / COMPLEX (DNA BINDING PROTEIN-DNA) / 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 / RSC-type complex / RNA polymerase II transcription regulatory region sequence-specific DNA binding / axon guidance / 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) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Fraenkel, E. / Rould, M.A. / Chambers, K.A. / Pabo, C.O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures. Authors: Fraenkel, E. / Rould, M.A. / Chambers, K.A. / Pabo, C.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hdd.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hdd.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hdd_validation.pdf.gz | 387.1 KB | Display | wwPDB validaton report |
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Full document | 3hdd_full_validation.pdf.gz | 392.5 KB | Display | |
Data in XML | 3hdd_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 3hdd_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hdd ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hdd | HTTPS FTP |
-Related structure data
Related structure data | 1hddS 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: 6387.157 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN / Source method: obtained synthetically Details: HOMEODOMAIN SEQUENCE FROM DROSOPHILA MELANOGASTER (FRUIT FLY) | ||
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#2: DNA chain | Mass: 6494.248 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN / Source method: obtained synthetically Details: HOMEODOMAIN SEQUENCE FROM DROSOPHILA MELANOGASTER (FRUIT FLY) | ||
#3: Protein | Mass: 7324.371 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 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: COMPLEX WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION OVER 0.26M AMOAC AND 1% PEG400., pH 7.0, vapor diffusion - hanging drop | |||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 15, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI MIRROR AND NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 18176 / % possible obs: 94 % / Redundancy: 2.6 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4 / % possible all: 70 |
Reflection | *PLUS Num. measured all: 47760 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 70 % |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1HDD Resolution: 2.2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 56.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.35 |