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Yorodumi- PDB-5h40: Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lach... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h40 | |||||||||
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Title | Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with sophorose | |||||||||
Components | Uncharacterized protein | |||||||||
Keywords | TRANSFERASE / beta-1 / 2-glucan / glycoside phosphorylase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium phytofermentans ISDg (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Nakajima, M. / Tanaka, N. / Furukawa, N. / Nihira, T. / Kodutsumi, Y. / Takahashi, Y. / Sugimoto, N. / Miyanaga, A. / Fushinobu, S. / Taguchi, H. / Nakai, H. | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans Authors: Nakajima, M. / Tanaka, N. / Furukawa, N. / Nihira, T. / Kodutsumi, Y. / Takahashi, Y. / Sugimoto, N. / Miyanaga, A. / Fushinobu, S. / Taguchi, H. / Nakai, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h40.cif.gz | 469.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h40.ent.gz | 378.3 KB | Display | PDB format |
PDBx/mmJSON format | 5h40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/5h40 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/5h40 | HTTPS FTP |
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-Related structure data
Related structure data | 5h3zSC 5h41C 5h42C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 1 - 1113 / Label seq-ID: 2 - 1114
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-Components
#1: Protein | Mass: 128481.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium phytofermentans ISDg (bacteria) Strain: ISDg / Gene: Cphy_0694 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A9KJS6, EC: 2.4.1.333 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-GOL / #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: 2.48 Å3/Da / Density % sol: 50.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG3350, Tris-HCl, calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 21, 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→86.02 Å / Num. obs: 123410 / % possible obs: 96.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 19944 / Num. unique all: 5677 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H3Z Resolution: 2.2→86.02 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.704 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.191 / 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: 27.695 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→86.02 Å
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Refine LS restraints |
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