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Open data
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Basic information
Entry | Database: PDB / ID: 2yop | ||||||
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Title | Long wavelength S-SAD structure of FAM3B PANDER | ||||||
![]() | PROTEIN FAM3B | ||||||
![]() | APOPTOSIS / FAM3 / DIABETES / ILEI / EMT | ||||||
Function / homology | ![]() insulin secretion / nuclear envelope lumen / cytokine activity / carbohydrate binding / apoptotic process / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johansson, P. / Bernstrom, J. / Gorman, T. / Oster, L. / Backstrom, S. / Schweikart, F. / Xu, B. / Xue, Y. / Holmberg Schiavone, L. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.9 KB | Display | ![]() |
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PDB format | ![]() | 98.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.4 KB | Display | ![]() |
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Full document | ![]() | 461.9 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 22161.145 Da / Num. of mol.: 3 / Fragment: RESIDUES 46-235 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: LONG WAVELENGTH TWO KAPPA ANGLE S-SAD |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.066 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30.56 Å / Num. obs: 32116 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 20.9 % / Biso Wilson estimate: 48.46 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / % possible all: 83.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.3→29.76 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.9038 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.268 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.201 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 46.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 16
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