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Yorodumi- PDB-6yqf: Crystal structure of the SYCE2-TEX12 delta-Ctip complex in a 4:4 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yqf | ||||||||||||
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Title | Crystal structure of the SYCE2-TEX12 delta-Ctip complex in a 4:4 assembly | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Synaptonemal complex meiosis recombination coiled-coil self-assembly SYCE2 TEX12 STRUCTURAL PROTEIN | ||||||||||||
Function / homology | Function and homology information meiotic DNA repair synthesis / central element / synaptonemal complex assembly / Meiotic synapsis / chromosome / cell division / nucleoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å | ||||||||||||
Authors | Dunce, J.M. / Davies, O.R. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2021 Title: Structural basis of meiotic chromosome synaptic elongation through hierarchical fibrous assembly of SYCE2-TEX12. Authors: Dunce, J.M. / Salmon, L.J. / Davies, O.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yqf.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yqf.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 6yqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/6yqf ftp://data.pdbj.org/pub/pdb/validation_reports/yq/6yqf | HTTPS FTP |
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-Related structure data
Related structure data | 6r17SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: Protein | Mass: 13180.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SYCE2, CESC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PIF2 #2: Protein | Mass: 7947.959 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEX12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXU0 |
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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: 2.36 Å3/Da / Density % sol: 47.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, 65% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9688 Å / Relative weight: 1 |
Reflection | Resolution: 3.327→47.452 Å / Num. obs: 4098 / % possible obs: 64.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 56.56 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.098 / Rrim(I) all: 0.246 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 3.327→3.594 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 342 / CC1/2: 0.516 / Rpim(I) all: 0.906 / Rrim(I) all: 2.445 / % possible all: 27.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R17 Resolution: 3.33→47.45 Å / SU ML: 0.3987 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.2763
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.52 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.33→47.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.33→47.45 Å
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