+Open data
-Basic information
Entry | Database: PDB / ID: 4zg0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mouse Syndesmos protein | ||||||
Components | Protein syndesmos | ||||||
Keywords | HYDROLASE / Nudix hydrolase / cytoplasmic protein / syndecan-4 cytoplasmic domain interactor | ||||||
Function / homology | negative regulation of double-strand break repair via nonhomologous end joining / snoRNA binding / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / nucleus / Alpha Beta / Tudor-interacting repair regulator protein Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å | ||||||
Authors | Lee, I. / Kim, H. / Yoo, J. / Cho, H. / Lee, W. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2015 Title: Crystal structure of syndesmos and its interaction with Syndecan-4 proteoglycan Authors: Kim, H. / Yoo, J. / Lee, I. / Kang, Y.J. / Cho, H.S. / Lee, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4zg0.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4zg0.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 4zg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/4zg0 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/4zg0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3couS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23502.262 Da / Num. of mol.: 2 / Fragment: UNP residues 8-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nudt16l1, Sdos / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8VHN8 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.88 % |
---|---|
Crystal grow | Temperature: 290 K / Method: batch mode / pH: 5.5 / Details: 0.2M Li sulfate, 0.1M Bis-Tris, 25%(m/w) PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 26347 / % possible obs: 96.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 34.79 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.155 / % possible all: 89.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3COU Resolution: 2.006→37.044 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 22.43 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.24 Å2 / Biso mean: 30.1055 Å2 / Biso min: 14.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.006→37.044 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|