+Open data
-Basic information
Entry | Database: PDB / ID: 7xq5 | ||||||
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Title | Crystal structure of ScIno2p-ScIno4p bound promoter DNA | ||||||
Components |
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Keywords | TRANSCRIPTION / Transcriptional regulators | ||||||
Function / homology | Function and homology information phospholipid biosynthetic process / RNA polymerase II transcription regulator complex / protein dimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Khan, M.H. / Lu, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Structural Analysis of Ino2p/Ino4p Mutual Interactions and Their Binding Interface with Promoter DNA. Authors: Khan, M.H. / Xue, L. / Yue, J. / Schuller, H.J. / Zhu, Z. / Niu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xq5.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xq5.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/7xq5 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/7xq5 | HTTPS FTP |
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-Related structure data
Related structure data | 5gnjS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 8996.399 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: INO4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13902 |
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#2: Protein | Mass: 8647.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: INO2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26798 |
-DNA chain , 2 types, 2 molecules CD
#3: DNA chain | Mass: 4593.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
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#4: DNA chain | Mass: 4583.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
-Non-polymers , 2 types, 80 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 4.59 Å3/Da / Density % sol: 73.22 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.01 M Cobalt (II) chloride hexahydrate, 0.1 M sodium acetate trihydrate, pH 5.0, 1.2 M 1, 6-hexandiol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97847 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97847 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→48.95 Å / Num. obs: 23995 / % possible obs: 99.42 % / Redundancy: 19.4 % / Biso Wilson estimate: 48.71 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 1.592 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2327 / CC1/2: 0.769 / Rpim(I) all: 0.374 / Rrim(I) all: 1.393 / % possible all: 98.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GNJ Resolution: 2.25→48.95 Å / SU ML: 0.283 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0213 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→48.95 Å
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Refine LS restraints |
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LS refinement shell |
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