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Yorodumi- PDB-6quf: Protein crystallization by ionic liquid hydrogel support: referen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6quf | ||||||
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Title | Protein crystallization by ionic liquid hydrogel support: reference crystal of glucose isomerase grown on standard silanized glass | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE / Glucose Isomerase / ionic liquid / structural comparison / hydration shell | ||||||
Function / homology | Function and homology information xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces rubiginosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | ||||||
Authors | Belviso, B.D. / Caliandro, R. / Caliandro, R. | ||||||
Citation | Journal: Crystals / Year: 2019 Title: Protein Crystallization in Ionic-Liquid Hydrogel Composite Membranes Authors: Belviso, B.D. / Caliandro, R. / Salehi, S.M. / di Profio, G. / Caliandro, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6quf.cif.gz | 334.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6quf.ent.gz | 271.2 KB | Display | PDB format |
PDBx/mmJSON format | 6quf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/6quf ftp://data.pdbj.org/pub/pdb/validation_reports/qu/6quf | HTTPS FTP |
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-Related structure data
Related structure data | 6qukC 1oadS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: Protein concentration 26mg/ml in HEPES 10mM pH 7 and MgCl2 1mM. reservoir: (NH4)2SO4 1.5M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97779 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2016 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97779 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→39.93 Å / Num. obs: 112879 / % possible obs: 76.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 8.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.03 / Rrim(I) all: 0.049 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.19→1.22 Å / Redundancy: 1 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 522 / CC1/2: 0.966 / Rpim(I) all: 0.166 / Rrim(I) all: 0.234 / % possible all: 4.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OAD Resolution: 1.19→39.93 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.979 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.032 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.397 Å2
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Refinement step | Cycle: 1 / Resolution: 1.19→39.93 Å
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Refine LS restraints |
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