+Open data
-Basic information
Entry | Database: PDB / ID: 5f7s | ||||||
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Title | Cycloalternan-degrading enzyme from Trueperella pyogenes | ||||||
Components | Glycoside hydrolase family 31 | ||||||
Keywords | 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: 2.3 Å | ||||||
Authors | Light, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Nat Microbiol / Year: 2016 Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis. Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.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 | 5f7s.cif.gz | 571.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f7s.ent.gz | 469.9 KB | Display | PDB format |
PDBx/mmJSON format | 5f7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f7s_validation.pdf.gz | 459.3 KB | Display | wwPDB validaton report |
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Full document | 5f7s_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 5f7s_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 5f7s_validation.cif.gz | 78.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/5f7s ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f7s | HTTPS FTP |
-Related structure data
Related structure data | 4kmqSC 5do8C 5f7pC 5f7qC 5f7rC 5f7uC 5f7vC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 82328.406 Da / Num. of mol.: 2 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 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-PEG / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.89 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: Protein solution: 12.0 mg/ml, 0.5 M NaCl, 0.01 M Tris-HCl pH 8.3 Crystallization condition: PACT (Qiagen) C11: 0.2 M Calcium chloride, 0.1 m Hepes pH 7, and 25% (w/v) PEG 600 |
-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 12, 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: 2.3→30 Å / Num. obs: 80180 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KMQ Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.291 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.196 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.376 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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