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Yorodumi- PDB-5o3z: Crystal structure of Sorbitol-6-Phosphate 2-dehydrogenase SrlD fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o3z | ||||||
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Title | Crystal structure of Sorbitol-6-Phosphate 2-dehydrogenase SrlD from Erwinia amylovora | ||||||
Components | Sorbitol-6-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Sorbitol-6-Phosphate 2-dehydrogenase / fire blight / Rosaceae | ||||||
Function / homology | Function and homology information sorbitol-6-phosphate 2-dehydrogenase / sorbitol-6-phosphate 2-dehydrogenase activity Similarity search - Function | ||||||
Biological species | Erwinia amylovora CFBP1430 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Salomone-Stagni, M. / Bartho, J.D. / Bellini, D. / Walsh, M.A. / Benini, S. | ||||||
Funding support | Italy, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2018 Title: Structural and functional analysis of Erwinia amylovora SrlD. The first crystal structure of a sorbitol-6-phosphate 2-dehydrogenase. Authors: Salomone-Stagni, M. / Bartho, J.D. / Kalita, E. / Rejzek, M. / Field, R.A. / Bellini, D. / Walsh, M.A. / Benini, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o3z.cif.gz | 582.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o3z.ent.gz | 481.4 KB | Display | PDB format |
PDBx/mmJSON format | 5o3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o3z_validation.pdf.gz | 520.3 KB | Display | wwPDB validaton report |
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Full document | 5o3z_full_validation.pdf.gz | 545.9 KB | Display | |
Data in XML | 5o3z_validation.xml.gz | 107.1 KB | Display | |
Data in CIF | 5o3z_validation.cif.gz | 151.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/5o3z ftp://data.pdbj.org/pub/pdb/validation_reports/o3/5o3z | HTTPS FTP |
-Related structure data
Related structure data | 1gegS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28162.064 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erwinia amylovora CFBP1430 (bacteria) / Gene: srlD, EAMY_3073 / Production host: Escherichia coli (E. coli) References: UniProt: D4I194, sorbitol-6-phosphate 2-dehydrogenase #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.53 % / Description: Rod |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: 100 mM HEPES pH 7.5, 600 mM MgCl2, 17% PEG3350 (cryo 20% Ethylene glycol) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→113.51 Å / Num. obs: 284126 / % possible obs: 99 % / Redundancy: 4.5 % / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.84→1.95 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.2 / % possible all: 97.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GEG Resolution: 1.84→113.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.073 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.152 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.31 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→113.51 Å
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Refine LS restraints |
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