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Yorodumi- PDB-7c5o: Crystal Structure of H177A mutant of Glyceraldehyde-3-phosphate-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c5o | |||||||||
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Title | Crystal Structure of H177A mutant of Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli complexed with NAD at 1.98 Angstrom resolution. | |||||||||
Components | Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / EcGAPDH 1 / NAD | |||||||||
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 / glucose metabolic process / NAD binding / NADP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli BL21 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å | |||||||||
Authors | 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 | China, 2items
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Citation | Journal: Biomolecules / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c5o.cif.gz | 506.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c5o.ent.gz | 418.8 KB | Display | PDB format |
PDBx/mmJSON format | 7c5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/7c5o ftp://data.pdbj.org/pub/pdb/validation_reports/c5/7c5o | HTTPS FTP |
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-Related structure data
Related structure data | 7c5gC 7c5hC 7c5iC 7c5jC 7c5kC 7c5lC 7c5mC 7c5nC 7c5pC 7c5qC 7c5rC 7c7kC 7c5fS 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: 37820.852 Da / Num. of mol.: 4 / Mutation: H177A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: ECBD_2224 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A140NCK4, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.43 Å3/Da / Density % sol: 49.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM sodium Cacodylate pH 6.5, 18%(w/v)PEG 1000, 200mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 98318 / % possible obs: 99.1 % / Redundancy: 20 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.98→2.01 Å / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 6.75 / Num. unique obs: 98318 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C5F Resolution: 1.981→48.175 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.981→48.175 Å
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Refine LS restraints |
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LS refinement shell |
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