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Yorodumi- PDB-5h3z: Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lach... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h3z | ||||||
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Title | Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans | ||||||
Components | Uncharacterized protein | ||||||
Keywords | TRANSFERASE / beta-1 / 2-glucan / glycoside phosphorylase | ||||||
Function / homology | Function and homology information transferase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium phytofermentans ISDg (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 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 | 5h3z.cif.gz | 468.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h3z.ent.gz | 388.9 KB | Display | PDB format |
PDBx/mmJSON format | 5h3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h3z_validation.pdf.gz | 466.7 KB | Display | wwPDB validaton report |
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Full document | 5h3z_full_validation.pdf.gz | 482.3 KB | Display | |
Data in XML | 5h3z_validation.xml.gz | 82.4 KB | Display | |
Data in CIF | 5h3z_validation.cif.gz | 119.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/5h3z ftp://data.pdbj.org/pub/pdb/validation_reports/h3/5h3z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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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: Chemical | ChemComp-GOL / #3: Chemical | #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: 2.53 Å3/Da / Density % sol: 51.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Tris-HCl, calcium acetate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97932 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 21, 2014 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 172867 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 2.8 / Num. unique all: 8557 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→42.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.04 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.14 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.95 Å2
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Refinement step | Cycle: 1 / Resolution: 2→42.72 Å
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Refine LS restraints |
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