+Open data
-Basic information
Entry | Database: PDB / ID: 6xdj | ||||||
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Title | Crystal Structure Analysis of MBP-SIN3 | ||||||
Components | Maltodextrin-binding protein,Transcriptional regulatory protein SIN3 | ||||||
Keywords | TRANSCRIPTION / RPD3 histone deacetylase complexes / epigenetic repression | ||||||
Function / homology | Function and homology information negative regulation of silent mating-type cassette heterochromatin formation / negative regulation of rDNA heterochromatin formation / Rpd3S complex / Rpd3L complex / Rpd3L-Expanded complex / rDNA chromatin condensation / nucleophagy / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / Sin3-type complex ...negative regulation of silent mating-type cassette heterochromatin formation / negative regulation of rDNA heterochromatin formation / Rpd3S complex / Rpd3L complex / Rpd3L-Expanded complex / rDNA chromatin condensation / nucleophagy / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / Sin3-type complex / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / double-strand break repair via nonhomologous end joining / transcription corepressor activity / nucleosome assembly / periplasmic space / transcription coactivator activity / cell cycle / cell division / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Serratia sp. (bacteria) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Seo, H.-S. / Dhe-Paganon, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal Structure Analysis of MBP-SIN3 Authors: Seo, H.-S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xdj.cif.gz | 632.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xdj.ent.gz | 524.7 KB | Display | PDB format |
PDBx/mmJSON format | 6xdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xdj_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6xdj_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6xdj_validation.xml.gz | 61.3 KB | Display | |
Data in CIF | 6xdj_validation.cif.gz | 87.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/6xdj ftp://data.pdbj.org/pub/pdb/validation_reports/xd/6xdj | HTTPS FTP |
-Related structure data
Related structure data | 4jbzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 48900.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia sp. (strain FS14) (bacteria), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: malE, SIN3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LXE0, UniProt: P22579 #2: Polysaccharide | #3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | #4: Water | ChemComp-HOH / | 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: 2.73 Å3/Da / Density % sol: 54.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris, pH 6.0, 1.6M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.2→75.841 Å / Num. obs: 105169 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 39.692 Å2 / Rpim(I) all: 0.062 / Rrim(I) all: 0.117 / Net I/σ(I): 7.8 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.4 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JBZ Resolution: 2.2→75.841 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.71 Å2 / Biso mean: 51.6779 Å2 / Biso min: 30.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→75.841 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 39.6121 Å / Origin y: 100.595 Å / Origin z: 115.2588 Å
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Refinement TLS group |
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