+Open data
-Basic information
Entry | Database: PDB / ID: 5iwz | ||||||
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Title | Synaptonemal complex protein | ||||||
Components | Synaptonemal complex protein 2 | ||||||
Keywords | CELL CYCLE / component of synaptonemal complexes | ||||||
Function / homology | Function and homology information meiotic nuclear division / male genitalia morphogenesis / male meiotic nuclear division / female meiotic nuclear division / synaptonemal complex / lateral element / fertilization / animal organ morphogenesis / cell division / negative regulation of apoptotic process ...meiotic nuclear division / male genitalia morphogenesis / male meiotic nuclear division / female meiotic nuclear division / synaptonemal complex / lateral element / fertilization / animal organ morphogenesis / cell division / negative regulation of apoptotic process / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.098 Å | ||||||
Authors | Feng, J. / Fu, S. / Cao, X. / Wu, H. / Lu, J. / Zeng, M. / Liu, L. / Yang, X. / Shen, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of synaptonemal complexes protein at 2.6 angstroms resolution Authors: Feng, J. / Fu, S. / Cao, X. / Wu, H. / Lu, J. / Zeng, M. / Liu, L. / Yang, X. / Shen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iwz.cif.gz | 165 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iwz.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 5iwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/5iwz ftp://data.pdbj.org/pub/pdb/validation_reports/iw/5iwz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46578.828 Da / Num. of mol.: 1 / Fragment: UNP residues 1-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sycp2, Scp2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CUU3 |
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#2: 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: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Tris-HCl pH 6.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 22, 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: 2→50 Å / Num. obs: 23639 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 20 |
-Processing
Software |
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Refinement | Resolution: 2.098→32.473 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.19 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.098→32.473 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: -7.0497 Å / Origin y: -15.0477 Å / Origin z: 19.144 Å
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Refinement TLS group | Selection details: all |