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Yorodumi- PDB-4a8i: Protein crystallization and microgravity: glucose isomerase cryst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a8i | ||||||
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Title | Protein crystallization and microgravity: glucose isomerase crystals grown during the PCDF-PROTEIN mission | ||||||
Components | XYLOSE ISOMERASE | ||||||
Keywords | ISOMERASE / MICROGRAVITY | ||||||
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: 0.95 Å | ||||||
Authors | Decanniere, K. / Patino-Lopez, L.-D. / Sleutel, M. / Evrard, C. / Van De Weerdt, C. / Haumont, E. / Gavira, J.A. / Otalora, F. / Maes, D. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a8i.cif.gz | 189.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a8i.ent.gz | 150.2 KB | Display | PDB format |
PDBx/mmJSON format | 4a8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/4a8i ftp://data.pdbj.org/pub/pdb/validation_reports/a8/4a8i | HTTPS FTP |
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-Related structure data
Related structure data | 4a8lC 4a8nC 4a8rC 2glkS C: citing same article (ref.) S: Starting model for refinement |
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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
#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 | ChemComp-EDO / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | 1,2-ETHANEDIOL (EDO): TENTATIVE. SOME DENSITY IN THE ACTIVE SITE COBALT (II) ION (CO): COBALT MOST ...1,2-ETHANEDIOL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % Description: STRUCTURE FACTOR FILE CONTAINS DATA TILL 0.775 ANGSTROM. |
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Crystal grow | pH: 7 Details: 32,7 MG/ML PROTEIN, 0.6 M AMMONIUM SULPHATE, 100 MM HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.775 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 19, 2011 / 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: 0.95→0.97 Å / Num. obs: 560892 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 2.6 |
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GLK Resolution: 0.95→70.87 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.323 / SU ML: 0.008 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.015 / 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: 11.379 Å2
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Refinement step | Cycle: LAST / Resolution: 0.95→70.87 Å
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Refine LS restraints |
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