[English] 日本語
Yorodumi- PDB-7dz5: Crystal structures of D-allulose 3-epimerase with D-sorbose from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dz5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structures of D-allulose 3-epimerase with D-sorbose 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 / alpha-D-Sorbopyranose / D-sorbose / D-tagatose 3-epimerase Function and homology information | ||||||
Biological species | Sinorhizobium fredii CCBAU 83666 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7dz5.cif.gz | 522 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7dz5.ent.gz | 347 KB | Display | PDB format |
PDBx/mmJSON format | 7dz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dz5_validation.pdf.gz | 5.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7dz5_full_validation.pdf.gz | 5.1 MB | Display | |
Data in XML | 7dz5_validation.xml.gz | 46.7 KB | Display | |
Data in CIF | 7dz5_validation.cif.gz | 66.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/7dz5 ftp://data.pdbj.org/pub/pdb/validation_reports/dz/7dz5 | HTTPS FTP |
-Related structure data
Related structure data | 7dz2C 7dz3C 7dz4C 7dz6C 5zfsS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31034.182 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 #2: Sugar | ChemComp-SDD / #3: Sugar | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.45 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43.97 Å / Num. obs: 150697 / % possible obs: 98.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.81 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.047 / Rrim(I) all: 0.089 / Net I/σ(I): 0.089 |
Reflection shell | Resolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1.9 / CC1/2: 0.756 / Rpim(I) all: 0.346 / Rrim(I) all: 0.671 / % possible all: 99.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZFS Resolution: 1.7→42.61 Å / SU ML: 0.1577 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.3469 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→42.61 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|