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Yorodumi- PDB-6n7f: 1.90 Angstrom Resolution Crystal Structure of Glutathione Reducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n7f | ||||||
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Title | 1.90 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus pyogenes in Complex with FAD. | ||||||
Components | Putative glutathione reductase (GR) | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Glutathione Reductase / FAD | ||||||
Function / homology | Function and homology information glutathione-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes serotype M1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Shabalin, I.G. / Grabowski, M. / Olphie, A. / Cardona-Correa, A. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.90 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus pyogenes in Complex with FAD. Authors: Minasov, G. / Shuvalova, L. / Shabalin, I.G. / Grabowski, M. / Olphie, A. / Cardona-Correa, A. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, 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 | 6n7f.cif.gz | 750 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n7f.ent.gz | 620.5 KB | Display | PDB format |
PDBx/mmJSON format | 6n7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/6n7f ftp://data.pdbj.org/pub/pdb/validation_reports/n7/6n7f | HTTPS FTP |
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-Related structure data
Related structure data | 5v36S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49246.750 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria) Gene: gor, SPy_0813 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9A0E2, glutathione-disulfide reductase |
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-Non-polymers , 7 types, 1736 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-RBF / | #4: Chemical | ChemComp-BTB / #5: Chemical | ChemComp-BCT / | #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-EDO / | #8: 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: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 9.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 1mM FAD; Screen: Classics II (F10), 0.2M Sodium chloride, 0.1M Bis-Tris pH=5.5, 25% (w/v) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2017 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 148744 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.058 / Rrim(I) all: 0.091 / Rsym value: 0.069 / Χ2: 1.014 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7256 / CC1/2: 0.657 / Rpim(I) all: 0.439 / Rrim(I) all: 0.681 / Rsym value: 0.517 / Χ2: 0.992 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V36 Resolution: 1.9→29.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.089 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.14 / 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: 26.814 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→29.47 Å
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