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Yorodumi- PDB-5jyf: Structures of Streptococcus agalactiae GBS GAPDH in different enz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jyf | ||||||
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Title | Structures of Streptococcus agalactiae GBS GAPDH in different enzymatic states | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / NAD / GAPDH / Glycolysis Apo Enzyme | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus agalactiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Schormann, N. / Chattopadhyay, D. | ||||||
Citation | Journal: PLoS ONE / Year: 2016 Title: Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes. Authors: Schormann, N. / Ayres, C.A. / Fry, A. / Green, T.J. / Banerjee, S. / Ulett, G.C. / Chattopadhyay, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jyf.cif.gz | 246.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jyf.ent.gz | 199.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/5jyf ftp://data.pdbj.org/pub/pdb/validation_reports/jy/5jyf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38214.867 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) Gene: gap, gapA, EN72_09590, ERS039640_00200, ERS046921_00390, RDF_1710 Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS References: UniProt: Q9ALW2, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor #2: 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: 2.06 Å3/Da / Density % sol: 40.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20-28% PEG4000, 0.1M Mes |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 5, 2014 / Details: Mirrors |
Radiation | Monochromator: Cryo-cooled double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→147.63 Å / Num. obs: 40180 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 52.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.62→2.76 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QX6_A Resolution: 2.62→89.55 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.893 / SU B: 19.431 / SU ML: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.375 / 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: 59.895 Å2
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Refinement step | Cycle: 1 / Resolution: 2.62→89.55 Å
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