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Yorodumi- PDB-4zli: Cellobionic acid phosphorylase - 3-O-beta-D-glucopyranosyl-alpha-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zli | |||||||||
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Title | Cellobionic acid phosphorylase - 3-O-beta-D-glucopyranosyl-alpha-D-glucopyranuronic acid complex | |||||||||
Components | Putative b-glycan phosphorylase | |||||||||
Keywords | TRANSFERASE / (alpha/alpha)6 barrel / glycoside hydrolase family 94 / oxidative cellulose degradation system / intracellular enzyme | |||||||||
Function / homology | Function and homology information hexosyltransferase activity / cellulose catabolic process / carbohydrate binding Similarity search - Function | |||||||||
Biological species | Saccharophagus degradans 2-40 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | |||||||||
Authors | Nam, Y.W. / Arakawa, T. / Fushinobu, S. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Crystal Structure and Substrate Recognition of Cellobionic Acid Phosphorylase, Which Plays a Key Role in Oxidative Cellulose Degradation by Microbes. Authors: Nam, Y.W. / Nihira, T. / Arakawa, T. / Saito, Y. / Kitaoka, M. / Nakai, H. / Fushinobu, S. #1: Journal: FEBS LETT. / Year: 2013 Title: Discovery of cellobionic acid phosphorylase in cellulolytic bacteria and fungi Authors: Nihira, T. / Saito, Y. / Nishimoto, M. / Kitaoka, M. / Igarashi, K. / Ohtsubo, K. / Nakai, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zli.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zli.ent.gz | 144.4 KB | Display | PDB format |
PDBx/mmJSON format | 4zli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zli_validation.pdf.gz | 835.3 KB | Display | wwPDB validaton report |
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Full document | 4zli_full_validation.pdf.gz | 842.3 KB | Display | |
Data in XML | 4zli_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 4zli_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/4zli ftp://data.pdbj.org/pub/pdb/validation_reports/zl/4zli | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) | ||||||||
Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 89782.922 Da / Num. of mol.: 1 / Mutation: M1G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharophagus degradans 2-40 (bacteria) Strain: 2-40 / Gene: cep94B / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus / References: UniProt: Q21MB1, EC: 2.4.1.321 |
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-alpha-D-glucopyranuronic acid Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 639 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / | #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: 3.47 Å3/Da / Density % sol: 64.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate (pH 5.6-6.0), 0.1 M Li2SO4, 0.6 M (NH3)2SO4, and 5% (v/v) glycerol PH range: 5.6-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9732 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 29, 2013 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9732 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 114626 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rsym value: 0.092 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→40.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.895 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.087 / 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: 28.168 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→40.5 Å
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