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Yorodumi- PDB-4wtp: Crystal structure of glycoside hydrolase family 17 beta-1,3-gluca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wtp | ||||||
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Title | Crystal structure of glycoside hydrolase family 17 beta-1,3-glucanosyltransferase from Rhizomucor miehei | ||||||
Components | beta-1,3-glucanosyltransferase | ||||||
Keywords | TRANSFERASE / beta-1 / 3-glucanosyltransferase / glycoside hydrolases family 17 / Rhizomucor miehei / Transglycosylation | ||||||
Function / homology | Glycoside hydrolase family 17 / Glycosyl hydrolases family 17 / cell wall / Transferases; Glycosyltransferases; Hexosyltransferases / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / Beta-1,3-glucanosyltransferase Function and homology information | ||||||
Biological species | Rhizomucor miehei CAU432 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å | ||||||
Authors | Qin, Z. / Yan, Q. / Lei, J. / Yang, S. / Jiang, Z. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: The first crystal structure of a glycoside hydrolase family 17 beta-1,3-glucanosyltransferase displays a unique catalytic cleft. Authors: Qin, Z. / Yan, Q. / Lei, J. / Yang, S. / Jiang, Z. / Wu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wtp.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wtp.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 4wtp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wtp_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 4wtp_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | 4wtp_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 4wtp_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/4wtp ftp://data.pdbj.org/pub/pdb/validation_reports/wt/4wtp | HTTPS FTP |
-Related 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: 32739.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizomucor miehei CAU432 (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0M3KKZ6*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | Sequence has been submitted to GenBank under accession number KP121406. N-terminal 34 residues are ...Sequence has been submitted to GenBank under accession number KP121406. N-terminal 34 residues are expression tags. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 25% (w/v) PEG 8000, 0.2M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.299→27.927 Å / Num. obs: 52655 / % possible obs: 92.39 % / Redundancy: 8.5 % / Net I/σ(I): 71.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.3→27.49 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.587 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.379 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→27.49 Å
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Refine LS restraints |
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