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Yorodumi- PDB-7c5f: Crystal Structure of Glyceraldehyde-3-phosphate dehydrogenase1 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c5f | |||||||||
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Title | Crystal Structure of Glyceraldehyde-3-phosphate dehydrogenase1 from Escherichia coli at 1.88 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: 1.88 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: Acta Crystallogr.,Sect.F / Year: 2020 Title: Characterization and structure of glyceraldehyde-3-phosphate dehydrogenase type 1 from Escherichia coli. 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c5f.cif.gz | 273.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c5f.ent.gz | 219.7 KB | Display | PDB format |
PDBx/mmJSON format | 7c5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/7c5f ftp://data.pdbj.org/pub/pdb/validation_reports/c5/7c5f | HTTPS FTP |
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-Related structure data
Related structure data | 3k73S S: Starting model for refinement |
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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: 37887.922 Da / Num. of mol.: 4 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: 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: 2.26 Å3/Da / Density % sol: 45.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100mM sodium acetate pH4.6, 30%(w/v) PEG 400, 200mM Ca(OAC)2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. obs: 114194 / % possible obs: 99.9 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 2 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 13.5 / Num. unique obs: 114194 / CC1/2: 0.526 / Rpim(I) all: 0.637 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K73 Resolution: 1.88→37.81 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.88→37.81 Å
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LS refinement shell | Highest resolution: 1.88 Å /
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