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- PDB-7c5p: Crystal Structure Glyceraldehyde-3-phosphate-dehydrogenase1 from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c5p | |||||||||
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Title | Crystal Structure Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli complexed with G3P at 2.35 Angstrom resolution. | |||||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase | |||||||||
![]() | OXIDOREDUCTASE / EcGAPDH 1 / NAD | |||||||||
Function / homology | ![]() Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, L. / Liu, M.R. / Bao, L.Y. / Yao, Y.C. / Bostrom, I.K. / Wang, Y.D. / Chen, A.Q. / Li, J.X. / Gu, S.H. / Ji, C.N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Novel Structures of Type 1 Glyceraldehyde-3-phosphate Dehydrogenase from Escherichia coli Provide New Insights into the Mechanism of Generation of 1,3-Bisphosphoglyceric Acid. Authors: Zhang, L. / Liu, M. / Bao, L. / Bostrom, K.I. / Yao, Y. / Li, J. / Gu, S. / Ji, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.5 KB | Display | ![]() |
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PDB format | ![]() | 224.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7c5gC ![]() 7c5hC ![]() 7c5iC ![]() 7c5jC ![]() 7c5kC ![]() 7c5lC ![]() 7c5mC ![]() 7c5nC ![]() 7c5oC ![]() 7c5qC ![]() 7c5rC ![]() 7c7kC ![]() 7c5fS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 4 molecules OPQR
#1: Protein | Mass: 37887.922 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A140NCK4, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 5 types, 633 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/G3H.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/G3H.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-G3H / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 100mM sodium PBS pH 6.1, 16%(w/v) PEG 1000, 200mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50.01 Å / Num. obs: 60156 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.35→2.39 Å / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 5632 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7C5F Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.655 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.221 / 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: 32.346 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→50 Å
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Refine LS restraints |
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