+Open data
-Basic information
Entry | Database: PDB / ID: 1jgg | ||||||
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Title | Even-skipped Homeodomain Complexed to AT-rich DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / EVEN-SKIPPED / HOMEODOMAIN / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information cephalic furrow formation / germ-band extension / regulation of myoblast fusion / blastoderm segmentation / periodic partitioning by pair rule gene / negative regulation of cardioblast cell fate specification / posterior head segmentation / trunk segmentation / adult heart development / motor neuron axon guidance ...cephalic furrow formation / germ-band extension / regulation of myoblast fusion / blastoderm segmentation / periodic partitioning by pair rule gene / negative regulation of cardioblast cell fate specification / posterior head segmentation / trunk segmentation / adult heart development / motor neuron axon guidance / regulation of axonogenesis / heart morphogenesis / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Hirsch, J.A. / Aggarwal, A.K. | ||||||
Citation | Journal: EMBO J. / Year: 1995 Title: Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity. Authors: Hirsch, J.A. / Aggarwal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jgg.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jgg.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jgg_validation.pdf.gz | 382.5 KB | Display | wwPDB validaton report |
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Full document | 1jgg_full_validation.pdf.gz | 392.6 KB | Display | |
Data in XML | 1jgg_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1jgg_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/1jgg ftp://data.pdbj.org/pub/pdb/validation_reports/jg/1jgg | 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: 3058.040 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 3027.030 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 7550.718 Da / Num. of mol.: 2 / Fragment: Homeodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / References: UniProt: P06602 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.36 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: sodium acetate, potassium chloride, DTT, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / Details: Hirsch, J.A., (1995) Proteins, 21, 268. / PH range low: 6.4 / PH range high: 5.8 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||
Reflection | Resolution: 2→15 Å / Num. all: 8613 / Num. obs: 8613 / % possible obs: 77.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.076 | ||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.186 / Num. unique all: 837 / % possible all: 52.4 | ||||||||||||
Reflection | *PLUS Num. measured all: 20689 | ||||||||||||
Reflection shell | *PLUS % possible obs: 52.4 % |
-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.229 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.016 |