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Yorodumi- PDB-7cqt: Crystal structure of Brassica juncea HMG-CoA synthase 1 mutant - ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cqt | ||||||
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Title | Crystal structure of Brassica juncea HMG-CoA synthase 1 mutant - S359A in complex with acetyl-CoA | ||||||
Components | 3-hydroxy-3-methylglutaryl coenzyme A synthase | ||||||
Keywords | TRANSFERASE / HMGS / S359A / mevalonate pathway / acetyl-CoA / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process / ergosterol biosynthetic process / identical protein binding Similarity search - Function | ||||||
Biological species | Brassica juncea (brown mustard) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Liao, P. / Hu, M. / Kong, G.K.W. / Hao, Q. / Chye, M.L. | ||||||
Funding support | Hong Kong, 1items
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Citation | Journal: Plant Cell.Physiol. / Year: 2021 Title: Overexpression and Inhibition of 3-Hydroxy-3-Methylglutaryl-CoA Synthase Affect Central Metabolic Pathways in Tobacco. Authors: Liao, P. / Lung, S.C. / Chan, W.L. / Hu, M. / Kong, G.K. / Bach, T.J. / Hao, Q. / Lo, C. / Chye, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cqt.cif.gz | 352 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cqt.ent.gz | 289.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cqt_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7cqt_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7cqt_validation.xml.gz | 69.8 KB | Display | |
Data in CIF | 7cqt_validation.cif.gz | 91.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/7cqt ftp://data.pdbj.org/pub/pdb/validation_reports/cq/7cqt | HTTPS FTP |
-Related structure data
Related structure data | 2f82S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 51095.938 Da / Num. of mol.: 4 / Mutation: S359A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brassica juncea (brown mustard) / Gene: HMGS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9M6U3, hydroxymethylglutaryl-CoA synthase #2: Chemical | #3: Chemical | ChemComp-A3P / | 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: 2.4 Å3/Da / Density % sol: 48.79 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 17% (wt to vol) PEG 20000, 0.27M, trimethylamine N-oxide, 100mM Pipes (pH 6.7), 2 mM DT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97939 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97939 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→34.624 Å / Num. obs: 44202 / % possible obs: 94.7 % / Redundancy: 3.71 % / Rsym value: 0.087 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.8→2.87 Å / Num. unique obs: 3158 / Rsym value: 0.087 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F82 Resolution: 2.8→34.624 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.8→34.624 Å
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