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Yorodumi- PDB-5b0s: Beta-1,2-Mannobiose phosphorylase from Listeria innocua - beta-1,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b0s | |||||||||
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Title | Beta-1,2-Mannobiose phosphorylase from Listeria innocua - beta-1,2-mannotriose complex | |||||||||
Components | Lin0857 protein | |||||||||
Keywords | TRANSFERASE / Glycoside phosphorylase | |||||||||
Function / homology | beta-1,2-mannobiose phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / glycosyltransferase activity / Beta-1,2-mannobiose phosphorylase Function and homology information | |||||||||
Biological species | Listeria innocua Clip11262 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Tsuda, T. / Arakawa, T. / Fushinobu, S. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: Febs Lett. / Year: 2015 Title: Characterization and crystal structure determination of beta-1,2-mannobiose phosphorylase from Listeria innocua Authors: Tsuda, T. / Nihira, T. / Chiku, K. / Suzuki, E. / Arakawa, T. / Nishimoto, M. / Kitaoka, M. / Nakai, H. / Fushinobu, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b0s.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b0s.ent.gz | 128.1 KB | Display | PDB format |
PDBx/mmJSON format | 5b0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/5b0s ftp://data.pdbj.org/pub/pdb/validation_reports/b0/5b0s | HTTPS FTP |
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-Related structure data
Related structure data | 5b0pC 5b0qC 5b0rC 1vkdS 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
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 41110.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria innocua Clip11262 (bacteria) / Strain: CLIP 11262 / Gene: lin0857 / Plasmid: pET24a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3)-RIL / References: UniProt: Q92DF6 #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 363 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 1.8 M (NH4)2SO4, 10 mM CoCl2, 0.1 M MES-NaOH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2014 |
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: 2.1→50 Å / Num. obs: 75403 / % possible obs: 100 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VKD Resolution: 2.1→43.44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.062 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.135 / 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: 39.357 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→43.44 Å
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