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Yorodumi- PDB-5mh1: Crystal structure of a DM9 domain containing protein from Crassos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mh1 | ||||||
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Title | Crystal structure of a DM9 domain containing protein from Crassostrea gigas | ||||||
Components | Natterin-3 | ||||||
Keywords | SUGAR BINDING PROTEIN / beta fold | ||||||
Function / homology | DM9 repeat / DM9 repeat / Repeats found in Drosophila proteins. / metal ion binding / beta-D-mannopyranose / Natterin-3 Function and homology information | ||||||
Biological species | Crassostrea gigas (Pacific oyster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Weinert, T. / Warkentin, E. / Pang, G. | ||||||
Citation | Journal: Front Immunol / Year: 2017 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. #1: Journal: To Be Published Title: A DM9 domain containing protein functions as a pattern recognition receptor with novel structural basis in Crassostrea gigas Authors: Jiang, S. / Huang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mh1.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mh1.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 5mh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mh1_validation.pdf.gz | 445.2 KB | Display | wwPDB validaton report |
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Full document | 5mh1_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 5mh1_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 5mh1_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/5mh1 ftp://data.pdbj.org/pub/pdb/validation_reports/mh/5mh1 | HTTPS FTP |
-Related structure data
Related structure data | 5mh0SC 5mh2C 5mh3C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15536.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: CGI_10011001, CGI_10018577 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: K1QRB6 | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Sugar | ChemComp-BMA / | ||
#4: Chemical | #5: 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: 2.31 Å3/Da / Density % sol: 46.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES, pH 6.0, 20% PEG 6000, 10 mM mannose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.999999 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999999 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→10 Å / Num. all: 985047 / Num. obs: 58075 / % possible obs: 99.9 % / Redundancy: 17 % / CC1/2: 0.99 / Rrim(I) all: 0.072 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 1.4 / Num. measured obs: 184866 / Num. unique all: 12761 / CC1/2: 0.806 / Rrim(I) all: 2 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MH0 Resolution: 1.1→5 Å / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 8.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→5 Å
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Refine LS restraints |
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