+Open data
-Basic information
Entry | Database: PDB / ID: 1akh | ||||||
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Title | MAT A1/ALPHA2/DNA TERNARY COMPLEX | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / COMPLEX (TWO DNA-BINDING PROTEINS-DNA) / COMPLEX / DNA-BINDING PROTEIN / DNA / TRANSCRIPTION REGULATION / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Li, T. / Jin, Y. / Vershon, A.K. / Wolberger, C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 1998 Title: Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract. Authors: Li, T. / Jin, Y. / Vershon, A.K. / Wolberger, C. #1: Journal: Proteins / Year: 1995 Title: Crystallization and Preliminary X-Ray Diffraction Studies of an A1/Alpha 2/DNA Ternary Complex Authors: Li, T. / Stark, M. / Johnson, A.D. / Wolberger, C. #2: 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. #3: Journal: Science / Year: 1995 Title: Erratum. Crystal Structure of the MATa1/MAT Alpha 2 Homeodomain Heterodimer Bound to DNA Authors: Li, T. / Stark, M.R. / 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 | 1akh.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1akh.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 1akh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1akh_validation.pdf.gz | 386.4 KB | Display | wwPDB validaton report |
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Full document | 1akh_full_validation.pdf.gz | 396.8 KB | Display | |
Data in XML | 1akh_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 1akh_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1akh ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1akh | HTTPS FTP |
-Related structure data
Related structure data | 1yrnS S: Starting model for refinement |
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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: 6413.210 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6466.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 7165.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MAT A1 RESIDUES 66 - 126 / Plasmid: PMS-K66 / Gene (production host): MAT A1 RESIDUES 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) Gene: MAT ALPHA2 RESIDUES 128 - 210 / Plasmid: PAV105 / Gene (production host): MAT ALPHA2 RESIDUES 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: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100MM HEPES PH 7.0, 20MM CACL2, 5MM [CO(NH3)6]CL3., VAPOR DIFFUSION, HANGING DROP, temperature 295.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 67.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||
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 / Type: RIGAKU RU200 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1995 |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 15656 / % possible obs: 83.6 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Rsym value: 7.4 |
Reflection shell | Resolution: 2.4→2.48 Å / % possible all: 67 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % possible obs: 83.6 % / Observed criterion σ(I): 1 / Num. measured all: 31013 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YRN Resolution: 2.5→6 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 34.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.58 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.324 |