[English] 日本語
Yorodumi- PDB-8jq5: Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jq5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with D-allulose | ||||||
Components | L-rhamnose isomerase | ||||||
Keywords | ISOMERASE / TIM barrel | ||||||
Function / homology | : / D-psicose / alpha-D-psicofuranose Function and homology information | ||||||
Biological species | Lacticaseibacillus rhamnosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Yoshida, H. / Yoshihara, A. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2024 Title: X-ray structure and characterization of a probiotic Lactobacillus rhamnosus Probio-M9 L-rhamnose isomerase. Authors: Yoshida, H. / Yamamoto, N. / Kurahara, L.H. / Izumori, K. / Yoshihara, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jq5.cif.gz | 698.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jq5.ent.gz | 578.7 KB | Display | PDB format |
PDBx/mmJSON format | 8jq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jq5_validation.pdf.gz | 8.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jq5_full_validation.pdf.gz | 8.1 MB | Display | |
Data in XML | 8jq5_validation.xml.gz | 64.9 KB | Display | |
Data in CIF | 8jq5_validation.cif.gz | 92.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/8jq5 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/8jq5 | HTTPS FTP |
-Related structure data
Related structure data | 8jq3C 8jq4C 8jq6C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
|
-Components
#1: Protein | Mass: 49746.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lacticaseibacillus rhamnosus (bacteria) Gene: rhaA / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 #2: Chemical | ChemComp-MN / #3: Sugar | ChemComp-PSJ / #4: Sugar | ChemComp-PSV / #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: 2.31 Å3/Da / Density % sol: 46.81 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG550MME, MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→48.94 Å / Num. obs: 192191 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.033 / Rrim(I) all: 0.123 / Χ2: 1.01 / Net I/σ(I): 17.5 / Num. measured all: 2569188 |
Reflection shell | Resolution: 1.73→1.76 Å / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 1.414 / Num. measured all: 127215 / Num. unique obs: 9422 / CC1/2: 0.722 / Rpim(I) all: 0.396 / Rrim(I) all: 1.469 / Χ2: 0.99 / Net I/σ(I) obs: 2.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→46.23 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.854 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.73→46.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|