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Yorodumi- PDB-2drp: THE CRYSTAL STRUCTURE OF A TWO ZINC-FINGER PEPTIDE REVEALS AN EXT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2drp | ||||||
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Title | THE CRYSTAL STRUCTURE OF A TWO ZINC-FINGER PEPTIDE REVEALS AN EXTENSION TO THE RULES FOR ZINC-FINGER/DNA RECOGNITION | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information dorsal trunk growth, open tracheal system / regulation of compound eye cone cell fate specification / R1/R6 development / compound eye corneal lens morphogenesis / branch fusion, open tracheal system / regulation of tube size, open tracheal system / chitin-based cuticle development / compound eye cone cell differentiation / R7 cell development / branching involved in open tracheal system development ...dorsal trunk growth, open tracheal system / regulation of compound eye cone cell fate specification / R1/R6 development / compound eye corneal lens morphogenesis / branch fusion, open tracheal system / regulation of tube size, open tracheal system / chitin-based cuticle development / compound eye cone cell differentiation / R7 cell development / branching involved in open tracheal system development / tracheal outgrowth, open tracheal system / regulation of embryonic cell shape / myoblast fate specification / follicle cell of egg chamber development / dorsal appendage formation / positive regulation of border follicle cell migration / polytene chromosome / peripheral nervous system development / positive regulation of DNA binding / transcription repressor complex / promoter-specific chromatin binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of cell shape / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Fairall, L. / Schwabe, J.W.R. / Chapman, L. / Finch, J.T. / Rhodes, D. | ||||||
Citation | Journal: Nature / Year: 1993 Title: The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition. Authors: Fairall, L. / Schwabe, J.W. / Chapman, L. / Finch, J.T. / Rhodes, D. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Sequence-Specific Binding by a Two Zinc-Finger Peptide from the Drosophila Melanogaster Tramtrack Protein Authors: Fairall, L. / Harrison, S.D. / Travers, A.A. / Rhodes, D. #2: Journal: Embo J. / Year: 1990 Title: The Tramtrack Gene Encodes a Drosophila Finger Protein that Interacts with the ftz Transcriptional Regulatory Region and Shows a Novel Embryonic Expression Pattern Authors: Harrison, S.D. / Travers, A.A. #3: Journal: Nucleic Acids Res. / Year: 1988 Title: Identification of the Binding Sites for Potential Regulatory Proteins in the Upstream Enhancer Element of the Drosophila Fushi Tarazu Gene Authors: Harrison, S.D. / Travers, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2drp.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2drp.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 2drp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2drp_validation.pdf.gz | 399 KB | Display | wwPDB validaton report |
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Full document | 2drp_full_validation.pdf.gz | 414.5 KB | Display | |
Data in XML | 2drp_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 2drp_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/2drp ftp://data.pdbj.org/pub/pdb/validation_reports/dr/2drp | 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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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5837.812 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 5785.757 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 8044.457 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: P17789 #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Sequence details | THE EXPRESSED CONSTRUCT IS NUMBERED 104 - 166 CORRESPONDING TO AMINO ACIDS 499 - 561 IN THE INTACT ...THE EXPRESSED CONSTRUCT IS NUMBERED 104 - 166 CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.14 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: small tubes / pH: 6 / Details: pH 6.00, SMALL TUBES / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: SIEMENS-NICOLET / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. all: 43552 / % possible obs: 99.2 % |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 11994 / % possible obs: 99.2 % / Rmerge(I) obs: 0.056 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.8→6 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.8→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 6 Å / Rfactor obs: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.76 |