+Open data
-Basic information
Entry | Database: PDB / ID: 2hdd | ||||||
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Title | ENGRAILED HOMEODOMAIN Q50K VARIANT 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 / MIRAS / Resolution: 1.9 Å | ||||||
Authors | Tucker-Kellogg, L. / Rould, M.A. / Chambers, K.A. / Ades, S.E. / Sauer, R.T. / Pabo, C.O. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity. Authors: Tucker-Kellogg, L. / Rould, M.A. / Chambers, K.A. / Ades, S.E. / Sauer, R.T. / 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 | 2hdd.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hdd.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 2hdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hdd_validation.pdf.gz | 382.9 KB | Display | wwPDB validaton report |
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Full document | 2hdd_full_validation.pdf.gz | 387.1 KB | Display | |
Data in XML | 2hdd_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 2hdd_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/2hdd ftp://data.pdbj.org/pub/pdb/validation_reports/hd/2hdd | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.703806, -0.704302, 0.092822), Vector: |
-Components
#1: DNA chain | Mass: 6389.133 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 6496.224 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 7426.592 Da / Num. of mol.: 2 / Mutation: Q50K 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: 3.23 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 .75M AMOAC AND 1% PEG400; DROP STARTS AT 1M AMOAC., pH 7.00, vapor diffusion - hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 48 % | |||||||||||||||||||||||||||||||||||
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 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI MIRROR + NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 27136 / % possible obs: 94 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.035 / Rsym value: 0.044 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.38 / % possible all: 84 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 94 % / Redundancy: 3.4 % |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 94 % / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.9→6 Å / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / % reflection Rfree: 10 % / Total num. of bins used: 10 / % reflection obs: 84 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |