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- PDB-2y0o: The structure of a D-lyxose isomerase from the sigmaB regulon of ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y0o | ||||||
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Title | The structure of a D-lyxose isomerase from the sigmaB regulon of Bacillus subtilis | ||||||
![]() | PROBABLE D-LYXOSE KETOL-ISOMERASE | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marles-Wright, J. / Lewis, R.J. | ||||||
![]() | ![]() Title: The Structure of a D-Lyxose Isomerase from the Sigmab Regulon of Bacillus Subtilis Authors: Marles-Wright, J. / Lewis, R.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.9 KB | Display | ![]() |
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PDB format | ![]() | 74.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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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: 20487.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ZINC AND ARSENIC COORDINATION IN ACTIVE SITE Source: (gene. exp.) ![]() ![]() ![]() Strain: 168 / Plasmid: PET28B / Production host: ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | ![]() #4: Chemical | ChemComp-ARS / | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 Details: 0.1 M SODIUM CACODYLATE PH 6.5 0.2 M NACL 2.0 M AMMONIUM SULFATE 1UL:1UL DROPS WITH PROTEIN IN WATER AT 11.5 MG/ML |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 24, 2010 / Details: MIRRORS |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.23→35.45 Å / Num. obs: 51297 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.23→1.3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: NONE Resolution: 1.229→34.872 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 16.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.657 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.229→34.872 Å
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Refine LS restraints |
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LS refinement shell |
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