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Yorodumi- PDB-3wdq: Crystal structure of beta-mannanase from a symbiotic protist of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wdq | ||||||
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Title | Crystal structure of beta-mannanase from a symbiotic protist of the termite Reticulitermes speratus | ||||||
Components | Beta-mannanase | ||||||
Keywords | HYDROLASE / Tim Barrel / Carbohydrate Binding | ||||||
Function / homology | Function and homology information substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase activity Similarity search - Function | ||||||
Biological species | Symbiotic protist of Reticulitermes speratus (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Tsukagoshi, H. / Ishida, T. / Touhara, K.K. / Igarashi, K. / Samejima, M. / Fushinobu, S. / Kitamoto, K. / Arioka, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural and Biochemical Analyses of Glycoside Hydrolase Family 26 beta-Mannanase from a Symbiotic Protist of the Termite Reticulitermes speratus Authors: Tsukagoshi, H. / Nakamura, A. / Ishida, T. / Touhara, K.K. / Otagiri, M. / Moriya, S. / Samejima, M. / Igarashi, K. / Fushinobu, S. / Kitamoto, K. / Arioka, M. #1: Journal: FEMS Microbiol.Ecol. / Year: 2007 Title: Environmental cDNA analysis of the genes involved in lignocellulose digestion in the symbiotic protist community of Reticulitermes speratus. Authors: Todaka, N. / Moriya, S. / Saita, K. / Hondo, T. / Kiuchi, I. / Takasu, H. / Piero, C. / Hayashizaki, Y. / Kudo, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wdq.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wdq.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/3wdq ftp://data.pdbj.org/pub/pdb/validation_reports/wd/3wdq | HTTPS FTP |
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-Related structure data
Related structure data | 3wdrC 3cbwS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 40256.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Symbiotic protist of Reticulitermes speratus (eukaryote) Gene: RsMan26C, RsManC / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H References: UniProt: H7CGE2, mannan endo-1,4-beta-mannosidase | ||||
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#2: Sugar | ChemComp-NAG / | ||||
#3: Chemical | #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 Å3/Da / Density % sol: 38.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG3350, 0.2M magnesium chloride, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 25, 2012 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 77823 / Num. obs: 77766 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.068 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3846 / Rsym value: 0.48 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CBW Resolution: 1.3→28.87 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.653 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.538 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.3→28.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.335 Å / Total num. of bins used: 20
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