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Yorodumi- PDB-5zfs: Crystal structure of Arthrobacter globiformis M30 sugar epimerase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zfs | ||||||
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Title | Crystal structure of Arthrobacter globiformis M30 sugar epimerase which can produce D-allulose from D-fructose | ||||||
Components | D-allulose-3-epimerase | ||||||
Keywords | ISOMERASE / Epimerase | ||||||
Function / homology | Function and homology information Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / racemase and epimerase activity, acting on carbohydrates and derivatives / manganese ion binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Arthrobacter globiformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Yoshida, H. / Yoshihara, A. / Gullapalli, P.K. / Ohtani, K. / Akimitsu, K. / Izumori, K. / Kamitori, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: X-ray structure of Arthrobacter globiformis M30 ketose 3-epimerase for the production of D-allulose from D-fructose. Authors: Yoshida, H. / Yoshihara, A. / Gullapalli, P.K. / Ohtani, K. / Akimitsu, K. / Izumori, K. / Kamitori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zfs.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zfs.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zfs_validation.pdf.gz | 452.6 KB | Display | wwPDB validaton report |
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Full document | 5zfs_full_validation.pdf.gz | 456.5 KB | Display | |
Data in XML | 5zfs_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 5zfs_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/5zfs ftp://data.pdbj.org/pub/pdb/validation_reports/zf/5zfs | HTTPS FTP |
-Related structure data
Related structure data | 3vylS S: Starting model for refinement |
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Similar 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: 32512.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: DAE / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: A0A1L7NQ96 #2: Chemical | #3: Chemical | ChemComp-ACT / #4: 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: 3.08 Å3/Da / Density % sol: 60.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: AMMONIUM ACETATE, SODIUM ACETATE TRIHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 27, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.96→45.02 Å / Num. obs: 59179 / % possible obs: 99 % / Redundancy: 22.556 % / Biso Wilson estimate: 28.637 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.08 / Χ2: 1.026 / Net I/σ(I): 31.46 / Num. measured all: 1334865 / Scaling rejects: 551 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VYL Resolution: 1.96→45.02 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.859 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 60.83 Å2 / Biso mean: 23.161 Å2 / Biso min: 7.81 Å2
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Refinement step | Cycle: final / Resolution: 1.96→45.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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