+Open data
-Basic information
Entry | Database: PDB / ID: 2yoq | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of FAM3B PANDER E30 construct | ||||||
Components | PROTEIN FAM3B | ||||||
Keywords | APOPTOSIS / DIABETES / ILEI / EMT | ||||||
Function / homology | Function and homology information insulin secretion / nuclear envelope lumen / cytokine activity / carbohydrate binding / apoptotic process / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Johansson, P. / Bernstrom, J. / Gorman, T. / Oster, L. / Backstrom, S. / Schweikart, F. / Xu, B. / Xue, Y. / Holmberg Schiavone, L. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Fam3B Pander and Fam3C Ilei Represent a Distinct Class of Signaling Molecules with a Non-Cytokine-Like Fold. Authors: Johansson, P. / Bernstrom, J. / Gorman, T. / Oster, L. / Backstrom, S. / Schweikart, F. / Xu, B. / Xue, Y. / Schiavone, L.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yoq.cif.gz | 123 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yoq.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 2yoq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yoq_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2yoq_full_validation.pdf.gz | 450.3 KB | Display | |
Data in XML | 2yoq_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 2yoq_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/2yoq ftp://data.pdbj.org/pub/pdb/validation_reports/yo/2yoq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 23974.236 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9D309 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.13 % / Description: NONE |
---|---|
Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→34.47 Å / Num. obs: 33513 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 42.49 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→21.64 Å / Cor.coef. Fo:Fc: 0.9457 / Cor.coef. Fo:Fc free: 0.9344 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.167 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.55 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.226 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→21.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.42 Å / Total num. of bins used: 17
|