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- PDB-6iqv: Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6iqv | ||||||
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Title | Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with Hg2+ from Lactobacillus plantarum | ||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase, type I | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoneda, K. / Kinoshita, H. | ||||||
![]() | ![]() Title: Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase from Lactobacillus plantarum: Insight into the Mercury Binding Mechanism Authors: Yoneda, K. / Ogata, M. / Nishiyama, K. / Fukuda, K. / Yasuda, S. / Igoshi, K. / Kinoshita, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 271.3 KB | Display | ![]() |
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PDB format | ![]() | 218.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.4 KB | Display | ![]() |
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Full document | ![]() | 519 KB | Display | |
Data in XML | ![]() | 55.7 KB | Display | |
Data in CIF | ![]() | 79.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iqmC ![]() 5j9gS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36475.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gap, HMPREF0531_11006 / Plasmid: pET28b / Production host: ![]() ![]() References: UniProt: D7VA33, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-HG / #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% (w/v) PEG 1500, 0.1M MIB buffer (pH 5.0) / PH range: 5 / Temp details: 293 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0085 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→101.86 Å / Num. obs: 90883 / % possible obs: 99.9 % / Redundancy: 9.1 % / Biso Wilson estimate: 37.34 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.13→2.17 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.521 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5J9G Resolution: 2.13→101.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.528 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 42.213 Å2
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Refinement step | Cycle: 1 / Resolution: 2.13→101.86 Å
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Refine LS restraints |
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