+Open data
-Basic information
Entry | Database: PDB / ID: 8hov | ||||||
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Title | Crystal structure of Hms1p from Saccharomyces cerevisiae | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / transcription factor / DNA binding domain / DNA binding protein / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information pseudohyphal growth / DNA-binding transcription activator activity / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||
Authors | Khan, M.H. / Wang, C.C. / Xue, L. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Hms1p from Saccharomyces cerevisiae Authors: Khan, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hov.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hov.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 8hov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hov_validation.pdf.gz | 487.7 KB | Display | wwPDB validaton report |
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Full document | 8hov_full_validation.pdf.gz | 493 KB | Display | |
Data in XML | 8hov_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 8hov_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/8hov ftp://data.pdbj.org/pub/pdb/validation_reports/ho/8hov | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 12582.369 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HMS1, YOR032C, OR26.22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12398 #2: DNA chain | Mass: 2386.593 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) #3: DNA chain | Mass: 2466.641 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) #4: 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: 3.26 Å3/Da / Density % sol: 62.28 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium citrate, pH 5.0, 8 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 16, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→50 Å / Num. obs: 28197 / % possible obs: 94.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 63.76 Å2 / CC1/2: 1 / Net I/σ(I): 16.47 |
Reflection shell | Resolution: 2.77→2.82 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1224 / Rpim(I) all: 0.371 / Rrim(I) all: 0.913 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→33.66 Å / SU ML: 0.4615 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.6316 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: 75.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.77→33.66 Å
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Refine LS restraints |
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LS refinement shell |
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