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Yorodumi- PDB-7bew: Glyceraldehyde 3-phosphate dehydrogenase from Campylobacter jejeu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bew | ||||||
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Title | Glyceraldehyde 3-phosphate dehydrogenase from Campylobacter jejeuni - NAD(P) complex | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Dehydrogenase Dual NAD/NADP specificity Glycolysis Gluconeogenesis | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding / NADP binding Similarity search - Function | ||||||
Biological species | Campylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å | ||||||
Authors | Moody, P.C.E. / Ayna, A. | ||||||
Citation | Journal: To Be Published Title: Crystal Structures of a dual coenzyme specific glyceraldehyde-3-phosphate dehydrogenase from the enteric pathogen Campylobacter jejuni Authors: Ayna, A. / Moody, P.C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bew.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bew.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 7bew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/7bew ftp://data.pdbj.org/pub/pdb/validation_reports/be/7bew | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36418.781 Da / Num. of mol.: 1 / Mutation: Ala 0 from tag Source method: isolated from a genetically manipulated source Details: ||Cj1403c|gapA|95980529 glyceraldehyde 3-phosphate dehydrogenase Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter) Strain: ATCC 700819 / NCTC 11168 / Gene: gapA, Cj1403c / Plasmid: pET151/D-gap / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: Q0P8L1, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor, aldehyde dehydrogenase [NAD(P)+], glyceraldehyde-3-phosphate dehydrogenase ...References: UniProt: Q0P8L1, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor, aldehyde dehydrogenase [NAD(P)+], glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) | ||||
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#2: Chemical | ChemComp-NAP / | ||||
#3: Chemical | ChemComp-PEG / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.67 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: PEG 4000 (20%), 0.3 M Na/K tartrate, 01.M Na Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→64.21 Å / Num. obs: 22791 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.25→2.35 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1658 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.25→57.797 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.141 / SU ML: 0.124 / Cross valid method: FREE R-VALUE / ESU R: 0.192 / ESU R Free: 0.174 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.316 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→57.797 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: 20
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