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Yorodumi- PDB-5do8: 1.8 Angstrom crystal structure of Listeria monocytogenes Lmo0184 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5do8 | ||||||
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Title | 1.8 Angstrom crystal structure of Listeria monocytogenes Lmo0184 alpha-1,6-glucosidase | ||||||
Components | Lmo0184 protein | ||||||
Keywords | HYDROLASE / Glycoside Hydrolase Family 13 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Listeria monocytogenes serovar 1/2a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Light, S.H. / Halavaty, A.S. / 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 | 5do8.cif.gz | 711.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5do8.ent.gz | 589.1 KB | Display | PDB format |
PDBx/mmJSON format | 5do8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5do8_validation.pdf.gz | 469.1 KB | Display | wwPDB validaton report |
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Full document | 5do8_full_validation.pdf.gz | 474.8 KB | Display | |
Data in XML | 5do8_validation.xml.gz | 74 KB | Display | |
Data in CIF | 5do8_validation.cif.gz | 113.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/5do8 ftp://data.pdbj.org/pub/pdb/validation_reports/do/5do8 | HTTPS FTP |
-Related structure data
Related structure data | 4kmqC 5f7pC 5f7qC 5f7rC 5f7sC 5f7uC 5f7vC 1uokS 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: 65337.453 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: lmo0184 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YAE6 #2: Sugar | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.67 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Crystallization condition: JCSG+ H8 (Qiagen) 0.1 M Am Acetate, 0.1 M Bis-tris (pH 5.5), 17% Peg 10000 Protein condition: 9 mg/ml + 10 mM Tris (pH 8.3), 500 mM NaCl, 50 mM glucose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 162894 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UOK Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.673 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.11 / 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: 22.386 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→30 Å
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Refine LS restraints |
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