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- PDB-8jq4: Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jq4 | ||||||
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Title | Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with L-rhamnose | ||||||
![]() | L-rhamnose isomerase | ||||||
![]() | ISOMERASE / TIM barrel | ||||||
Function / homology | : / alpha-L-rhamnopyranose / beta-L-rhamnopyranose![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoshida, H. / Yoshihara, A. | ||||||
Funding support | 1items
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 720.2 KB | Display | ![]() |
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PDB format | ![]() | 595.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 71.5 KB | Display | |
Data in CIF | ![]() | 105.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jq3C ![]() 8jq5C ![]() 8jq6C 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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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 49746.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rhaA / Plasmid: pQE60 / Production host: ![]() ![]() #2: Chemical | ChemComp-MN / #3: Sugar | ChemComp-RM4 / #4: Sugar | #5: 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: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 550MME, MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.61→46.93 Å / Num. obs: 241662 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.033 / Rrim(I) all: 0.12 / Χ2: 1.04 / Net I/σ(I): 16.7 / Num. measured all: 3204608 |
Reflection shell | Resolution: 1.61→1.64 Å / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 1.402 / Num. measured all: 159575 / Num. unique obs: 11906 / CC1/2: 0.711 / Rpim(I) all: 0.397 / Rrim(I) all: 1.458 / Χ2: 1.01 / Net I/σ(I) obs: 2.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 19.681 Å2
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Refinement step | Cycle: 1 / Resolution: 1.61→45.1 Å
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Refine LS restraints |
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