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- PDB-7dz6: Crystal structures of D-allulose 3-epimerase with D-allulose from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dz6 | ||||||
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Title | Crystal structures of D-allulose 3-epimerase with D-allulose from Sinorhizobium fredii | ||||||
![]() | D-tagatose 3-epimerase | ||||||
![]() | 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-psicose / D-tagatose 3-epimerase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, Z.L. / Miyakawa, T. / Tanokura, M. / Lu, F.P. / Qin, H.-M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 508.2 KB | Display | ![]() |
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PDB format | ![]() | 339.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 41.3 KB | Display | |
Data in CIF | ![]() | 57.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dz2C ![]() 7dz3C ![]() 7dz4C ![]() 7dz5C ![]() 5zfsS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: SF83666_b55120 / Production host: ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting 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: ![]() ![]() ![]() |
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: 2.1→48.41 Å / Num. obs: 79743 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 34.62 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4533 / CC1/2: 0.752 / Rpim(I) all: 0.399 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZFS Resolution: 2.1→37.15 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4762 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: 43.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→37.15 Å
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Refine LS restraints |
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LS refinement shell |
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