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- PDB-7dmm: Structure of a glucose isomerase crystal grown in an aqueous glyc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dmm | ||||||
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Title | Structure of a glucose isomerase crystal grown in an aqueous glycerol solution without any precipitants | ||||||
![]() | Xylose isomerase | ||||||
![]() | ISOMERASE / ISOMERASE(INTRAMOLEC | ||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, Y. / Maita, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Extraordinarily fast growth of high-quality glucose isomerase crystals simply by concentration in a precipitant-free solution with a cryoprotectant Authors: Suzuki, Y. / Ikemitsu, N. / Maita, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101 KB | Display | ![]() |
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PDB format | ![]() | 74.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1xibS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43065.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: precipitant-free in 30(v/v)% aqueous glycerol solution |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→70.94 Å / Num. obs: 256074 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 0.99→1.01 Å / Rmerge(I) obs: 0.308 / Num. unique obs: 12629 / CC1/2: 0.94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XIB Resolution: 0.99→51.16 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.246 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 9.953 Å2
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Refinement step | Cycle: 1 / Resolution: 0.99→51.16 Å
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Refine LS restraints |
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