+Open data
-Basic information
Entry | Database: PDB / ID: 4zle | ||||||
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Title | Cellobionic acid phosphorylase - ligand free structure | ||||||
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: 2.1 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 | 4zle.cif.gz | 181.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zle.ent.gz | 141 KB | Display | PDB format |
PDBx/mmJSON format | 4zle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zle_validation.pdf.gz | 457.3 KB | Display | wwPDB validaton report |
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Full document | 4zle_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 4zle_validation.xml.gz | 33 KB | Display | |
Data in CIF | 4zle_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/4zle ftp://data.pdbj.org/pub/pdb/validation_reports/zl/4zle | 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
#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: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-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 % / Description: Hexagonal bypyramid |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: sodium citrate, Li2SO4, 0.6 M (NH3)2SO4, 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: 0.9988 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 12, 2013 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9988 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 72225 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rsym value: 0.112 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→41.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.147 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.157 / 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: 30.548 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→41.44 Å
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