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- PDB-5xd8: Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xd8 | ||||||
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Title | Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase | ||||||
![]() | 3,6-anhydro-alpha-L-galactonate cycloisomerase | ||||||
![]() | ISOMERASE / Enolase superfamily / 3 / 6-anhydro-L-galactonate cycloisomerase / lyase / barrel domain / capping domain | ||||||
Function / homology | ![]() 3,6-anhydro-L-galactonate cycloisomerase / galactose catabolic process / hydro-lyase activity / isomerase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, S. / Choi, I.-G. / Kim, H.-Y. | ||||||
![]() | ![]() Title: Crystal structure analysis of 3,6-anhydro-l-galactonate cycloisomerase suggests emergence of novel substrate specificity in the enolase superfamily Authors: Lee, S. / Kim, K.H. / Kim, H.-Y. / Choi, I.-G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.9 KB | Display | ![]() |
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PDB format | ![]() | 118.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.5 KB | Display | ![]() |
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Full document | ![]() | 451.9 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xd7C ![]() 5xd9C ![]() 2ovlS C: citing same article ( S: Starting model for refinement |
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Similar 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: 41320.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: H2IFX0, 3,6-anhydro-L-galactonate cycloisomerase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M magnesium chloride hexahydrate, 0.2 M Bis/Tris (pH 6.5) and 25% (w/v) polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 262988 / % possible obs: 99 % / Redundancy: 9.5 % / Net I/σ(I): 43.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OVL Resolution: 2.505→39.139 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 31.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.505→39.139 Å
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Refine LS restraints |
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LS refinement shell |
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