+Open data
-Basic information
Entry | Database: PDB / ID: 2r5y | ||||||
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Title | Structure of Scr/Exd complex bound to a consensus Hox-Exd site | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Homeodomain / homeotic proteins / specificity / Developmental protein / DNA-binding / Homeobox / Nucleus / Transcription / Transcription regulation / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information sex comb development / salivary gland boundary specification / oenocyte development / somatic muscle development / eye development / regulation of cell fate specification / peripheral nervous system development / anterior/posterior pattern specification / midgut development / transcription factor binding ...sex comb development / salivary gland boundary specification / oenocyte development / somatic muscle development / eye development / regulation of cell fate specification / peripheral nervous system development / anterior/posterior pattern specification / midgut development / transcription factor binding / neuron development / embryonic organ development / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription coregulator activity / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / RNA polymerase II transcription regulator complex / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Aggarwal, A.K. / Passner, J.M. / Jain, R. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2007 Title: Functional specificity of a Hox protein mediated by the recognition of minor groove structure Authors: Joshi, R. / Passner, J.M. / Rohs, R. / Jain, R. / Sosinsky, A. / Crickmore, M.A. / Jacob, V. / Aggarwal, A.K. / Honig, B. / Mann, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r5y.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r5y.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 2r5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/2r5y ftp://data.pdbj.org/pub/pdb/validation_reports/r5/2r5y | HTTPS FTP |
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-Related structure data
Related structure data | 2r5zC 1b8iS S: Starting model for refinement C: citing same article (ref.) |
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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: 6154.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 6110.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 10967.711 Da / Num. of mol.: 1 / Fragment: Homeobox DNA-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Scr / Plasmid: pET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P09077 |
#4: Protein | Mass: 7553.561 Da / Num. of mol.: 1 / Fragment: Homeobox TALE-type DNA-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: exd / Plasmid: pET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS / References: UniProt: P40427 |
#5: 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: 3.47 Å3/Da / Density % sol: 64.54 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 20% MPD, 10-14% PEG 4000, 0.2M sodium acetate, 0.2M potassium chloride, 0.1M Tris , pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2004 / Details: double crystal monochromator |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 13684 / Num. obs: 13550 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Redundancy: 23.2 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 36 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 9.7 / Num. unique all: 1371 / Rsym value: 0.356 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1B8I Resolution: 2.6→11.96 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 541221.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.2994 Å2 / ksol: 0.308333 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→11.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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