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Yorodumi- PDB-6m5x: A fungal glyceraldehyde-3-phosphate dehydrogenase with self-resis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m5x | ||||||
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Title | A fungal glyceraldehyde-3-phosphate dehydrogenase with self-resistance to inhibitor heptelidic acid | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / inhibitor / self-resistance / heptelidic acid | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Hypocrea virens (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05990923752 Å | ||||||
Authors | Yan, Y. / Zang, X. / Cooper, S.J. / Lin, H. / Zhou, J. / Tang, Y. | ||||||
Citation | Journal: Chem Sci / Year: 2020 Title: Biosynthesis of the fungal glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid and mechanism of self-resistance Authors: Yan, Y. / Zang, X. / Cooper, S.J. / Lin, H. / Zhou, J. / Tang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m5x.cif.gz | 346.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m5x.ent.gz | 227.5 KB | Display | PDB format |
PDBx/mmJSON format | 6m5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m5x_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6m5x_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6m5x_validation.xml.gz | 55.1 KB | Display | |
Data in CIF | 6m5x_validation.cif.gz | 77.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/6m5x ftp://data.pdbj.org/pub/pdb/validation_reports/m5/6m5x | HTTPS FTP |
-Related structure data
Related structure data | 6m61C 4o59S 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 ORPQ
#1: Protein | Mass: 36021.844 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypocrea virens (strain Gv29-8 / FGSC 10586) (fungus) Strain: Gv29-8 / FGSC 10586 / Gene: TRIVIDRAFT_217322 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: G9NDK9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) |
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-Non-polymers , 6 types, 688 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.45 Å3/Da / Density % sol: 49.76 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M sodium acetate, 0.1M HEPES pH 7.5, 22% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.059→50 Å / Num. obs: 85148 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 25.100858583 Å2 / CC1/2: 0.837 / Rmerge(I) obs: 0.126 / Net I/σ(I): 2.429 |
Reflection shell | Resolution: 2.06→2.1 Å / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.429 / Num. unique obs: 85148 / CC1/2: 0.837 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O59 Resolution: 2.05990923752→39.2901171738 Å / SU ML: 0.196588078964 / Cross valid method: FREE R-VALUE / σ(F): 1.36645748307 / Phase error: 19.557254141
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.7337282741 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05990923752→39.2901171738 Å
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Refine LS restraints |
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LS refinement shell |
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