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- PDB-6h86: Rebuilt and re-refined PDB entry 4R3Q: Crystal structure of SYCE3 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6h86 | |||||||||
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Title | Rebuilt and re-refined PDB entry 4R3Q: Crystal structure of SYCE3 | |||||||||
![]() | Synaptonemal complex central element protein 3 | |||||||||
![]() | STRUCTURAL PROTEIN / Meiosis / synaptonemal complex | |||||||||
Function / homology | ![]() positive regulation of developmental process / central element / positive regulation of reproductive process / synaptonemal complex assembly / reciprocal meiotic recombination / ectopic germ cell programmed cell death / chromosome / spermatogenesis / positive regulation of apoptotic process / cell division ...positive regulation of developmental process / central element / positive regulation of reproductive process / synaptonemal complex assembly / reciprocal meiotic recombination / ectopic germ cell programmed cell death / chromosome / spermatogenesis / positive regulation of apoptotic process / cell division / apoptotic process / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Davies, O.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A molecular model for self-assembly of the synaptonemal complex protein SYCE3. Authors: Dunne, O.M. / Davies, O.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.5 KB | Display | ![]() |
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PDB format | ![]() | 86.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 429.5 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 10480.013 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M Citric acid, 7% 2-propanol, 1% PEG 20000, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 16498 / % possible obs: 96.89 % / Redundancy: 3.9 % / Rsym value: 0.059 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.9→1.93 Å / Rsym value: 0.486 |
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Processing
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Refinement | Resolution: 1.901→23.661 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 25.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→23.661 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 31.5493 Å / Origin y: -11.0764 Å / Origin z: -0.2192 Å
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Refinement TLS group | Selection details: all |