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Yorodumi- PDB-4wpg: Group A Streptococcus GacA is an essential dTDP-4-dehydrorhamnose... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wpg | ||||||
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Title | Group A Streptococcus GacA is an essential dTDP-4-dehydrorhamnose reductase (RmlD) | ||||||
Components | dTDP-4-dehydrorhamnose reductase | ||||||
Keywords | OXIDOREDUCTASE / RmlD / dTDP-4-dehydrorhamnose reductase | ||||||
Function / homology | Function and homology information dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / dTDP-rhamnose biosynthetic process Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å | ||||||
Authors | van der Beek, S.L. / Le Breton, Y. / Ferenbach, A.T. / van Aalten, D.M.F. / Navratilova, I. / McIver, K. / van Sorge, N.M. / Dorfmueller, H.C. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2015 Title: GacA is essential for Group A Streptococcus and defines a new class of monomeric dTDP-4-dehydrorhamnose reductases (RmlD). Authors: van der Beek, S.L. / Le Breton, Y. / Ferenbach, A.T. / Chapman, R.N. / van Aalten, D.M. / Navratilova, I. / Boons, G.J. / McIver, K.S. / van Sorge, N.M. / Dorfmueller, H.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wpg.cif.gz | 251.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wpg.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 4wpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/4wpg ftp://data.pdbj.org/pub/pdb/validation_reports/wp/4wpg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32535.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: GacA / Plasmid: pGEXHIS6 / Details (production host): His6GST / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: T0BV37, UniProt: Q9A0G6*PLUS, dTDP-4-dehydrorhamnose reductase |
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#2: Chemical | ChemComp-MPD / ( |
#3: Chemical | ChemComp-MRD / ( |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.45 % / Description: bar |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M ...Details: PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M sodium oxamate) and 0.1 M MES/imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.89 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→43.8 Å / Num. obs: 108172 / % possible obs: 94.03 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.1→1.14 Å / Mean I/σ(I) obs: 5.7 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Resolution: 1.1→43.77 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.031 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / 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: 17.021 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→43.77 Å
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Refine LS restraints |
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