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Yorodumi- PDB-5v8y: Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v8y | ||||||
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Title | Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NAD / GAPDH / GLYCOLYSIS | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Schormann, N. / Ulett, G.C. / Chattopadhyay, D. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) Authors: Schormann, N. / 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 | 5v8y.cif.gz | 281.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v8y.ent.gz | 227.2 KB | Display | PDB format |
PDBx/mmJSON format | 5v8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/5v8y ftp://data.pdbj.org/pub/pdb/validation_reports/v8/5v8y | HTTPS FTP |
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-Related structure data
Related structure data | 5v8xC 5jyfS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 38069.664 Da / Num. of mol.: 2 / Mutation: K298I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) Gene: gap, AX245_09885, DX05_09270, EN72_09590, RDF_1710, TH70_1537 Plasmid: pET15b / Cell line (production host): Rosetta(DE3)pLysS / Production host: Escherichia coli (E. coli) References: UniProt: Q9ALW2, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-MG / | #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: 2.72 Å3/Da / Density % sol: 54.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 3350, 0.2M MgCl2, 0.1 M Mes pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2017 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 52755 / % possible obs: 90.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 25.62 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.04 / Rrim(I) all: 0.108 / Χ2: 2.31 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.822 / CC1/2: 0.655 / Rpim(I) all: 0.492 / Rrim(I) all: 0.964 / Χ2: 1.212 / % possible all: 76.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JYF Resolution: 1.95→34.667 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.47 Å2 / Biso mean: 34.4409 Å2 / Biso min: 12.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→34.667 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 38.3972 Å / Origin y: -42.063 Å / Origin z: 21.0677 Å
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Refinement TLS group |
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