+Open data
-Basic information
Entry | Database: PDB / ID: 3r3s | ||||||
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Title | Structure of the YghA Oxidoreductase from Salmonella enterica | ||||||
Components | oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / 3-layer(aba) sandwich / Rossmann fold / NAD(P)-binding Rossmann-like domain | ||||||
Function / homology | Function and homology information : / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of the YghA Oxidoreductase from Salmonella enterica Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r3s.cif.gz | 490.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r3s.ent.gz | 396.5 KB | Display | PDB format |
PDBx/mmJSON format | 3r3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/3r3s ftp://data.pdbj.org/pub/pdb/validation_reports/r3/3r3s | HTTPS FTP |
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-Related structure data
Related structure data | 3i3oS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 31470.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: yghA, STM3157 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8ZM09 |
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-Non-polymers , 5 types, 1956 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-SO4 / | #6: 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: 2.29 Å3/Da / Density % sol: 46.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2 M ammonium sulfate, 100 mM Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 2, 2010 / Details: beryllium lens | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→50 Å / Num. all: 313957 / Num. obs: 311759 / % possible obs: 99.3 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3I3O Resolution: 1.25→27.34 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.12 / σ(F): 1.44 / σ(I): 2.2 / Phase error: 13.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.916 Å2 / ksol: 0.434 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.56 Å2 / Biso mean: 11.78 Å2 / Biso min: 3.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→27.34 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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