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- PDB-4a8n: Protein crystallization and microgravity: glucose isomerase cryst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a8n | ||||||
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Title | Protein crystallization and microgravity: glucose isomerase crystals grown during the PCDF-PROTEIN mission | ||||||
![]() | XYLOSE ISOMERASE | ||||||
![]() | ISOMERASE / MICROGRAVITY | ||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Decanniere, K. / Patino-Lopez, L.-D. / Sleutel, M. / Evrard, C. / Van De Weerdt, C. / Haumont, E. / Gavira, J.A. / Otalora, F. / Maes, D. | ||||||
![]() | ![]() Title: Protein Crystallization and Microgravity: Glucose Isomerase Crystals Grown During the Pcdf-Protein Mission Authors: Decanniere, K. / Patino-Lopez, L.-D. / Sleutel, M. / Evrard, C. / Van De Weerdt, C. / Haumont, E. / Gavira, J.A. / Otalora, F. / Maes, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.1 KB | Display | ![]() |
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PDB format | ![]() | 149.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.7 KB | Display | ![]() |
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Full document | ![]() | 448.2 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a8iC ![]() 4a8lC ![]() 4a8rC ![]() 2glkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | COBALT (II) ION (CO): COBALT MOST LIKELY GIVEN ANOMALOUS DIFFRACTION AT 2 WAVELENGTHS GLYCEROL (GOL) ...COBALT (II) ION (CO): COBALT MOST LIKELY GIVEN ANOMALOUS DIFFRACTIO | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % Description: STRUCTURE FILE CONTAINS FREER-REFLECTIONS TO 0.9 A (NO ACTUAL DATA).ONE CONSISTENT FREER SET WAS USED FOR SEVERAL DATA SETS. |
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Crystal grow | pH: 7 Details: 28.7 MG/ML PROTEIN, 1.4 MG/ML PROTEIN COVALENTLY LABELED WITH BIS(2,2'-BIPYRIDINE)-4,4'-DICARBOXY BIPYRIDINE-RUTHENIUM DI(N-SUCCINIMIDYL ESTER) BIS(HEXAFLUOROPHOSPHATE), 0.9M AMMONIUM ...Details: 28.7 MG/ML PROTEIN, 1.4 MG/ML PROTEIN COVALENTLY LABELED WITH BIS(2,2'-BIPYRIDINE)-4,4'-DICARBOXY BIPYRIDINE-RUTHENIUM DI(N-SUCCINIMIDYL ESTER) BIS(HEXAFLUOROPHOSPHATE), 0.9M AMMONIUM SULPHATE, 100MM HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 19, 2009 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.775 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→1.23 Å / Num. obs: 280608 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2GLK Resolution: 1.2→70.77 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.59 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.016 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→70.77 Å
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Refine LS restraints |
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