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Yorodumi- PDB-4zb0: A dehydrated form of glucose isomerase collected at room temperature. -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zb0 | ||||||
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Title | A dehydrated form of glucose isomerase collected at room temperature. | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE | ||||||
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: 2 Å | ||||||
Authors | Sandy, J. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: A generic protocol for protein crystal dehydration using the HC1b humidity controller. Authors: Lobley, C.M. / Sandy, J. / Sanchez-Weatherby, J. / Mazzorana, M. / Krojer, T. / Nowak, R.P. / Sorensen, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zb0.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zb0.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 4zb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/4zb0 ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zb0 | HTTPS FTP |
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-Related structure data
Related structure data | 4zb2C 4zb5C 4zbcC 1mnzS 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: 43152.105 Da / Num. of mol.: 2 / Fragment: UNP residues 2-388 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase #2: Chemical | ChemComp-MN / #3: Sugar | #4: Sugar | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Hepes, 10% PEG 400, 0.05 M Manganese Chloride, 20% Glucose |
-Data collection
Diffraction | Mean temperature: 293 K Ambient temp details: Collected using HC1b humidity control device at RH of 96% |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2015 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→68.38 Å / Num. obs: 53324 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4 / Num. measured all: 169888 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 5.9 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MNZ Resolution: 2→68.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.183 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.132 / 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: 20.946 Å2
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Refinement step | Cycle: LAST / Resolution: 2→68.38 Å
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Refine LS restraints |
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