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Yorodumi- PDB-1yrn: CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2 HOMEODOMAIN HETERODIMER ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yrn | ||||||
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Title | CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2 HOMEODOMAIN HETERODIMER BOUND TO DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / COMPLEX / DNA-BINDING PROTEIN / DNA / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information : / regulation of mating-type specific transcription, DNA-templated / RNA polymerase II transcription repressor complex / DNA binding, bending / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II ...: / regulation of mating-type specific transcription, DNA-templated / RNA polymerase II transcription repressor complex / DNA binding, bending / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Li, T. / Stark, M.R. / Johnson, A.D. / Wolberger, C. | ||||||
Citation | Journal: Science / Year: 1995 Title: Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. Authors: Li, T. / Stark, M.R. / Johnson, A.D. / Wolberger, C. #1: Journal: Proteins / Year: 1995 Title: Crystallization and Preliminary X-Ray Diffraction Studies of an A1/alpha2/DNA Ternary Complex Authors: Li, T. / Stark, M. / Johnson, A.D. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yrn.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yrn.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 1yrn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yrn_validation.pdf.gz | 388.5 KB | Display | wwPDB validaton report |
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Full document | 1yrn_full_validation.pdf.gz | 404.5 KB | Display | |
Data in XML | 1yrn_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1yrn_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/1yrn ftp://data.pdbj.org/pub/pdb/validation_reports/yr/1yrn | 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: 6395.183 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6484.246 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 7164.493 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Description: T7 PROMOTER / Gene: MAT A1 RESIDUE 66-126 / Plasmid: PMS/K66 / Gene (production host): MAT A1 RESIDUE 66-126 / Production host: Escherichia coli (E. coli) / References: UniProt: P01366, UniProt: P0CY10*PLUS |
#4: Protein | Mass: 9773.306 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Description: TAC PROMOTER / Gene: MAT ALPHA2 RESIDUE 128-210 / Plasmid: PAV105 / Gene (production host): MAT ALPHA2 RESIDUE 128-210 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B2C0, UniProt: P0CY08*PLUS |
#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: 3.84 Å3/Da / Density % sol: 67.6 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 67.6 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 94 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 23, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 18106 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.055 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % possible obs: 94 % / Redundancy: 4 % / Num. measured all: 76841 |
-Processing
Software |
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Refinement | Resolution: 2.5→6 Å / σ(F): 2
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Displacement parameters | Biso mean: 33.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |