+Open data
-Basic information
Entry | Database: PDB / ID: 1qp9 | ||||||
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Title | STRUCTURE OF HAP1-PC7 COMPLEXED TO THE UAS OF CYC7 | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / ZINC BINUCLEAR CLUSTER / COILED-COIL / HEPTAD REPEAT / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Lukens, A. / King, D. / Marmorstein, R. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2000 Title: Structure of HAP1-PC7 bound to DNA: implications for DNA recognition and allosteric effects of DNA-binding on transcriptional activation. Authors: Lukens, A.K. / King, D.A. / Marmorstein, R. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein Authors: King, D. / Zhang, L. / Guarente, L. / Marmorstein, R. #2: Journal: Nat.Struct.Biol. / Year: 1999 Title: Structure of HAP-18-DNA implicates direct allosteric effect of protein-DNA interactions on transcriptional activation Authors: King, D. / Zhang, L. / Guarente, L. / Marmorstein, R. #3: Journal: Thesis / Year: 1999 Title: Asymmetric binding and transactivation properties of the HAP1 DNA binding domain Authors: King, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qp9.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qp9.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qp9_validation.pdf.gz | 406.9 KB | Display | wwPDB validaton report |
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Full document | 1qp9_full_validation.pdf.gz | 426.8 KB | Display | |
Data in XML | 1qp9_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 1qp9_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/1qp9 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/1qp9 | 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: 6098.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE NATURALLY OCCURING IN YEAST #2: DNA chain | Mass: 6166.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE NATURALLY OCCURING IN YEAST #3: Protein | Mass: 9087.827 Da / Num. of mol.: 4 / Fragment: HAP1-PC7 DNA BINDING DOMAIN, RESIDUES 55-130 / Mutation: S63G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PRSET-A / Production host: Escherichia coli (E. coli) / References: UniProt: P12351, UniProt: P0CS82*PLUS #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.68 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 11% PEG 400, 10 MM MGSO4, 200 MM KCL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.917 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Sep 11, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 27006 / Num. obs: 27006 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 14.77 % / Biso Wilson estimate: 60.054 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 2.75→2.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.167 / % possible all: 100 |
Reflection | *PLUS Num. obs: 14650 / Num. measured all: 27006 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Resolution: 2.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |