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Yorodumi- PDB-7c5g: Crystal Structure of C150S mutant of Glyceraldehyde-3-phosphate-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c5g | |||||||||
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Title | Crystal Structure of C150S mutant of Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli complexed with PO4 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: 1.98 Å | |||||||||
Authors | Zhang, L. / Liu, M.R. / 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 | 7c5g.cif.gz | 287.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c5g.ent.gz | 230.9 KB | Display | PDB format |
PDBx/mmJSON format | 7c5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/7c5g ftp://data.pdbj.org/pub/pdb/validation_reports/c5/7c5g | HTTPS FTP |
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-Related structure data
Related structure data | 7c5hC 7c5iC 7c5jC 7c5kC 7c5lC 7c5mC 7c5nC 7c5oC 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
-Protein , 1 types, 4 molecules OPQR
#1: Protein | Mass: 37871.855 Da / Num. of mol.: 4 / Mutation: C150S 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 |
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-Non-polymers , 5 types, 1037 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.28 Å3/Da / Density % sol: 46.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 100mM sodium Cacodylate pH 6.3, 20%(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: 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: 1.98→50 Å / Num. obs: 90257 / % possible obs: 90.8 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 13.57 |
Reflection shell | Resolution: 1.98→2.01 Å / Rmerge(I) obs: 0.559 / Num. unique obs: 90257 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C5F Resolution: 1.98→45 Å / SU B: 3.409 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.151 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.03 Å / Total num. of bins used: 20
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