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Yorodumi- PDB-5aye: Crystal structure of Ruminococcus albus beta-(1,4)-mannooligosacc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aye | |||||||||
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Title | Crystal structure of Ruminococcus albus beta-(1,4)-mannooligosaccharide phosphorylase (RaMP2) in complexes with phosphate and beta-(1,4)-mannobiose | |||||||||
Components | Beta-1,4-mannooligosaccharide phosphorylase | |||||||||
Keywords | TRANSFERASE / Glycoside hydrolase family 130 | |||||||||
Function / homology | Function and homology information beta-1,4-mannooligosaccharide phosphorylase / glycosyltransferase activity / cell wall organization / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Ruminococcus albus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Ye, Y. / Saburi, W. / Kato, K. / Yao, M. | |||||||||
Citation | Journal: Febs Lett. / Year: 2016 Title: Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies. Authors: Ye, Y. / Saburi, W. / Odaka, R. / Kato, K. / Sakurai, N. / Komoda, K. / Nishimoto, M. / Kitaoka, M. / Mori, H. / Yao, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aye.cif.gz | 433.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aye.ent.gz | 353.8 KB | Display | PDB format |
PDBx/mmJSON format | 5aye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/5aye ftp://data.pdbj.org/pub/pdb/validation_reports/ay/5aye | HTTPS FTP |
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-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: 38352.293 Da / Num. of mol.: 6 / Fragment: UNP residues 1-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus albus (strain ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7) (bacteria) Strain: ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7 / Gene: Rumal_0099 / Production host: Escherichia coli (E. coli) References: UniProt: E6UBR9, beta-1,4-mannooligosaccharide phosphorylase #2: Polysaccharide | beta-D-mannopyranose-(1-4)-beta-D-mannopyranose / 4beta-beta-mannobiose #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium phosphate, 0.1M Tris-HCl buffer, 50%(v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.18 Å / Num. obs: 123824 / % possible obs: 99.4 % / Redundancy: 3.8 % / Net I/σ(I): 8.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.086 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→47.086 Å
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Refine LS restraints |
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LS refinement shell |
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