+Open data
-Basic information
Entry | Database: PDB / ID: 4zbc | |||||||||
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Title | A dehydrated form of glucose isomerase collected at 100K. | |||||||||
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 | 4zbc.cif.gz | 178.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zbc.ent.gz | 140.2 KB | Display | PDB format |
PDBx/mmJSON format | 4zbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zbc_validation.pdf.gz | 477.5 KB | Display | wwPDB validaton report |
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Full document | 4zbc_full_validation.pdf.gz | 489.5 KB | Display | |
Data in XML | 4zbc_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 4zbc_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/4zbc ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zbc | HTTPS FTP |
-Related structure data
Related structure data | 4zb0C 4zb2C 4zb5C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 43283.297 Da / Num. of mol.: 2 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 | ChemComp-GLC / #4: Sugar | ChemComp-FRU / #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: 2.16 Å3/Da / Density % sol: 43.14 % |
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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 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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→67.58 Å / Num. obs: 50965 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 8.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MNZ Resolution: 2→67.58 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.95 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.138 / 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: 14.877 Å2
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Refinement step | Cycle: 1 / Resolution: 2→67.58 Å
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Refine LS restraints |
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