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Open data
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Basic information
Entry | Database: PDB / ID: 7bjz | |||||||||
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Title | GLUCOSE ISOMERASE S171W in H32 | |||||||||
![]() | Xylose isomerase | |||||||||
![]() | ISOMERASE | |||||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sleutel, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Nucleation of protein mesocrystals via oriented attachment. Authors: Van Driessche, A.E.S. / Van Gerven, N. / Joosten, R.R.M. / Ling, W.L. / Bacia, M. / Sommerdijk, N. / Sleutel, M. #1: ![]() Title: Nonclassical nucleation of protein mesocrystals via oriented attachment Authors: Van Driessche, A.E.S. / Van Gerven, N. / Joosten, R.R.M. / Sommerdijk, A.J.M. / Sleutel, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.9 KB | Display | ![]() |
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PDB format | ![]() | 126.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9xiaS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 43353.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.75 % |
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Crystal grow | Temperature: 294 K / Method: batch mode Details: 30 mg.mL-1 50mM Hepes 7.0 100mM MgCl2 8% (w/v) PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→55.87 Å / Num. obs: 44769 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.998 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.13→2.19 Å / Num. unique obs: 3281 / CC1/2: 0.562 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 9XIA Resolution: 2.13→55.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.08 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.192 / 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: 48.006 Å2
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Refinement step | Cycle: 1 / Resolution: 2.13→55.87 Å
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Refine LS restraints |
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