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Yorodumi- PDB-5i0g: Cycloalternan-degrading enzyme from Trueperella pyogenes in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i0g | |||||||||
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Title | Cycloalternan-degrading enzyme from Trueperella pyogenes in complex with cycloalternan | |||||||||
Components | Glycoside hydrolase family 31 | |||||||||
Keywords | SUGAR BINDING PROTEIN / Hydrolase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Trueperella pyogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Light, S.H. / Minasov, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: Structure / Year: 2017 Title: Transferase Versus Hydrolase: The Role of Conformational Flexibility in Reaction Specificity. Authors: Light, S.H. / Cahoon, L.A. / Mahasenan, K.V. / Lee, M. / Boggess, B. / Halavaty, A.S. / Mobashery, S. / Freitag, N.E. / Anderson, W.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i0g.cif.gz | 302.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i0g.ent.gz | 244.5 KB | Display | PDB format |
PDBx/mmJSON format | 5i0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/5i0g ftp://data.pdbj.org/pub/pdb/validation_reports/i0/5i0g | HTTPS FTP |
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-Related structure data
Related structure data | 5hopC 5hpoC 5hxmC 5i0dC 5i0eC 5i0fC 5f7sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 82284.398 Da / Num. of mol.: 1 / Mutation: D532A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trueperella pyogenes (bacteria) / Gene: CQ11_05330 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: X4QP62 |
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#2: Polysaccharide | Cyclic alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-SIN / |
#4: 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: 2.78 Å3/Da / Density % sol: 55.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein solution: 5.3 mg/ml, 0.25 M NaCl, 0.01 M Tris-HCl pH 8.3 Crystallization condition: JCSG+ (Qiagen) G7: 0.1 M Succinic acid (pH 7.0) and 15% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 48835 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 1.9 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F7S Resolution: 2.15→28.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.788 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.17 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.656 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→28.48 Å
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Refine LS restraints |
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