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Yorodumi- PDB-1tvz: Crystal structure of 3-hydroxy-3-methylglutaryl-coenzyme A syntha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tvz | ||||||
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Title | Crystal structure of 3-hydroxy-3-methylglutaryl-coenzyme A synthase from Staphylococcus aureus | ||||||
Components | 3-hydroxy-3-methylglutaryl-CoA synthase | ||||||
Keywords | LYASE / HMG-CoA synthase / HMGS / coenzyme A / thiolase fold / condensing enzyme / cholesterol biosynthesis | ||||||
Function / homology | Function and homology information hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2 Å | ||||||
Authors | Campobasso, N. / Patel, M. / Wilding, I.E. / Kallender, H. / Rosenberg, M. / Gwynn, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Staphylococcus aureus 3-hydroxy-3-methylglutaryl-CoA synthase: crystal structure and mechanism Authors: Campobasso, N. / Patel, M. / Wilding, I.E. / Kallender, H. / Rosenberg, M. / Gwynn, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tvz.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tvz.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tvz_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 1tvz_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 1tvz_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 1tvz_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/1tvz ftp://data.pdbj.org/pub/pdb/validation_reports/tv/1tvz | HTTPS FTP |
-Related 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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Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: -x+1, -y, z |
-Components
#1: Protein | Mass: 43326.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mvaS / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) References: GenBank: 9937361, UniProt: Q9FD87*PLUS, EC: 4.1.3.5 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: TRIS, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 10, 2000 |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→99 Å / Num. obs: 32374 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 6.5 / Rsym value: 0.27 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.911 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.151 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.907 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20 /
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