+Open data
-Basic information
Entry | Database: PDB / ID: 6bzg | ||||||
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Title | Structure of S. cerevisiae Zip2:Spo16 complex, P212121 form | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / XPF-ERCC1 / Meiosis / Recombination | ||||||
Function / homology | Function and homology information regulation of synaptonemal complex assembly / synapsis initiation complex / regulation of reciprocal meiotic recombination / DNA secondary structure binding / ascospore formation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / positive regulation of protein sumoylation / homologous recombination ...regulation of synaptonemal complex assembly / synapsis initiation complex / regulation of reciprocal meiotic recombination / DNA secondary structure binding / ascospore formation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / positive regulation of protein sumoylation / homologous recombination / reciprocal meiotic recombination / protein sumoylation / condensed nuclear chromosome / nucleotide binding / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å | ||||||
Authors | Arora, K. / Corbett, K.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: The conserved XPF:ERCC1-like Zip2:Spo16 complex controls meiotic crossover formation through structure-specific DNA binding. Authors: Arora, K. / Corbett, K.D. #1: Journal: Biorxiv / Year: 2018 Title: Structure of Zip2:Spo16, a conserved XPF:ERCC1-like complex critical for meiotic crossover formation Authors: Arora, K. / Corbett, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bzg.cif.gz | 178.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bzg.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 6bzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/6bzg ftp://data.pdbj.org/pub/pdb/validation_reports/bz/6bzg | HTTPS FTP |
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-Related structure data
Related structure data | 6bzfC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/539 / Data set type: diffraction image data |
Experimental dataset #2 | Data reference: 10.15785/SBGRID/540 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24345.135 Da / Num. of mol.: 1 / Mutation: K641A, E642A, K643A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ZIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P53061 | ||||
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#2: Protein | Mass: 23023.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPO16 / Production host: Escherichia coli (E. coli) / References: UniProt: P17122 | ||||
#3: Chemical | #4: Chemical | ChemComp-P6G / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Bis Tris pH 5.5, 200 mM Ammonium sulfate, 15% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→100 Å / Num. obs: 28219 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.987 / Rsym value: 0.207 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.13→2.19 Å / Num. unique obs: 15501 / CC1/2: 0.484 / Rsym value: 2.074 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.13→69.809 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 32.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→69.809 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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