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Open data
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Basic information
Entry | Database: PDB / ID: 1de5 | ||||||
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Title | L-RHAMNOSE ISOMERASE | ||||||
![]() | L-RHAMNOSE ISOMERASE | ||||||
![]() | ISOMERASE / (BETA8/ALPHA8) BARREL / TIM BARREL / HYDRIDE SHIFT | ||||||
Function / homology | ![]() L-rhamnose isomerase / rhamnose binding / L-rhamnose isomerase activity / L-lyxose metabolic process / rhamnose catabolic process / manganese ion binding / protein homotetramerization / protein-containing complex / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Korndorfer, I.P. / Fessner, W.D. / Matthews, B.W. | ||||||
![]() | ![]() Title: The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution. Authors: Korndorfer, I.P. / Fessner, W.D. / Matthews, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 357.7 KB | Display | ![]() |
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PDB format | ![]() | 287.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 494.7 KB | Display | ![]() |
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Full document | ![]() | 597.5 KB | Display | |
Data in XML | ![]() | 82.6 KB | Display | |
Data in CIF | ![]() | 115.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 48170.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Sugar | ChemComp-RNT / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.26 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.2 M CITRATE, 0.1-M HEPES, 22.5 - 30.0 % PEG 8000, 10 % ISOPROPANOL, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 195 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. all: 156599 / Num. obs: 85683 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2 % / % possible all: 88 |
Reflection shell | *PLUS % possible obs: 88 % |
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Processing
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Refinement | Resolution: 2.2→15 Å / Stereochemistry target values: TNT
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.154 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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