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Yorodumi- PDB-8pof: The crystal structure of RsSymEG1 reveals a unique form of smalle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pof | ||||||
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Title | The crystal structure of RsSymEG1 reveals a unique form of smaller GH7 endoglucanases alongside GH7 cellobiohydrolases in protist symbionts of termites | ||||||
Components | Putative glycosyl hydrolase family7 | ||||||
Keywords | HYDROLASE / GH7 / endoglucanase / cellulase | ||||||
Function / homology | Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / Putative glycosyl hydrolase family7 Function and homology information | ||||||
Biological species | Reticulitermes speratus gut symbiotic protist (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Haataja, T. / Sandgren, M. / Hansson, H. / Stahlberg, J. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Febs J. / Year: 2024 Title: The crystal structure of RsSymEG1 reveals a unique form of smaller GH7 endoglucanases alongside GH7 cellobiohydrolases in protist symbionts of termites. Authors: Haataja, T. / Hansson, H. / Moriya, S. / Sandgren, M. / Stahlberg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pof.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pof.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 8pof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pof_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
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Full document | 8pof_full_validation.pdf.gz | 421.2 KB | Display | |
Data in XML | 8pof_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8pof_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/8pof ftp://data.pdbj.org/pub/pdb/validation_reports/po/8pof | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 33954.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Reticulitermes speratus gut symbiotic protist (eukaryote) Production host: Aspergillus oryzae (mold) / References: UniProt: A4UWN6 |
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#2: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.03 M Sodium fluoride, 0.03 M Sodium bromide, 0.03 M Sodium iodide, 12% v/v PEG 500 MME, 6 % w/v PEG 20000, 0.1 M Tris-Bicine pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 21, 2021 / Details: KB mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→45.8 Å / Num. obs: 27804 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC1/2: 0.996 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.85→1.89 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1666 / CC1/2: 0.821 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→45.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.111 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.646 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→45.8 Å
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Refine LS restraints |
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LS refinement shell |
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