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- PDB-5mh2: Crystal structure of a DM9 domain containing protein from Crassos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mh2 | ||||||
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Title | Crystal structure of a DM9 domain containing protein from Crassostrea gigas with D22A mutation | ||||||
![]() | Natterin-3 | ||||||
![]() | SUGAR BINDING PROTEIN / beta fold | ||||||
Function / homology | DM9 repeat / DM9 repeat / Repeats found in Drosophila proteins. / Natterin-3![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weinert, T. / Warkentin, E. / Peng, G. | ||||||
![]() | ![]() Title: DM9 Domain Containing Protein Functions As a Pattern Recognition Receptor with Broad Microbial Recognition Spectrum. Authors: Jiang, S. / Wang, L. / Huang, M. / Jia, Z. / Weinert, T. / Warkentin, E. / Liu, C. / Song, X. / Zhang, H. / Witt, J. / Qiu, L. / Peng, G. / Song, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.5 KB | Display | ![]() |
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PDB format | ![]() | 188.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mh0SC ![]() 5mh1C ![]() 5mh3C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15492.688 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-GOL / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.11 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES, 30% PEG 3350, 0.12M Magnisium Chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.3→20 Å / Num. obs: 106083 / % possible obs: 98.9 % / Redundancy: 6.3 % / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.5 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5MH0 Resolution: 1.3→19.6 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→19.6 Å
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Refine LS restraints |
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LS refinement shell |
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