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Yorodumi- PDB-7dz3: Crystal structures of D-allulose 3-epimerase with D-fructose from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dz3 | ||||||
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Title | Crystal structures of D-allulose 3-epimerase with D-fructose from Sinorhizobium fredii | ||||||
Components | D-tagatose 3-epimerase | ||||||
Keywords | ISOMERASE / D-allulose / rare sugar / Sinorhizobium fredii / D-allulose 3-epimerase | ||||||
Function / homology | racemase and epimerase activity, acting on carbohydrates and derivatives / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / manganese ion binding / D-fructose / D-tagatose 3-epimerase Function and homology information | ||||||
Biological species | Sinorhizobium fredii CCBAU 83666 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Zhu, Z.L. / Miyakawa, T. / Tanokura, M. / Lu, F.P. / Qin, H.-M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Substantial Improvement of an Epimerase for the Synthesis of D-Allulose by Biosensor-Based High-Throughput Microdroplet Screening Authors: Li, C. / Gao, X. / Qi, H. / Zhang, W. / Li, L. / Wei, C. / Wei, M. / Sun, X. / Wang, S. / Wang, L. / Ji, Y. / Mao, S. / Zhu, Z. / Tanokura, M. / Lu, F. / Qin, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dz3.cif.gz | 510.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dz3.ent.gz | 343.1 KB | Display | PDB format |
PDBx/mmJSON format | 7dz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dz3_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 7dz3_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 7dz3_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 7dz3_validation.cif.gz | 61.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/7dz3 ftp://data.pdbj.org/pub/pdb/validation_reports/dz/7dz3 | HTTPS FTP |
-Related structure data
Related structure data | 7dz2C 7dz4C 7dz5C 7dz6C 5zfsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31336.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium fredii CCBAU 83666 (bacteria) Gene: SF83666_b55120 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta References: UniProt: A0A249Q1V1, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives #2: Chemical | ChemComp-MG / #3: Sugar | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.84 Å3/Da / Density % sol: 56.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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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: Dec 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→48.78 Å / Num. obs: 116087 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.54 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.046 / Rrim(I) all: 0.123 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.88→1.91 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 5634 / CC1/2: 0.716 / Rpim(I) all: 0.481 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZFS Resolution: 1.88→44.92 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1815 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→44.92 Å
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Refine LS restraints |
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LS refinement shell |
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