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Yorodumi- PDB-3v4x: The Biochemical and Structural Basis for Inhibition of Enterococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v4x | ||||||
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Title | The Biochemical and Structural Basis for Inhibition of Enterococcus faecalis HMG-CoA Synthase, mvaS, by Hymeglusin | ||||||
Components | HMG-CoA synthase | ||||||
Keywords | Transferase/Inhibitor / HYDROXYMETHYLGLUTARYL-CoA SYNTHASE / Hymeglusin covalent adduct / Transferase-Inhibitor complex | ||||||
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 Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 Å | ||||||
Authors | Skaff, D.A. / Ramyar, K.X. / McWhorter, W.J. / Geisbrecht, B.V. / Miziorko, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Biochemical and structural basis for inhibition of Enterococcus faecalis hydroxymethylglutaryl-CoA synthase, mvaS, by hymeglusin. Authors: Skaff, D.A. / Ramyar, K.X. / McWhorter, W.J. / Barta, M.L. / Geisbrecht, B.V. / Miziorko, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v4x.cif.gz | 858.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v4x.ent.gz | 733.7 KB | Display | PDB format |
PDBx/mmJSON format | 3v4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v4x_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3v4x_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3v4x_validation.xml.gz | 70.6 KB | Display | |
Data in CIF | 3v4x_validation.cif.gz | 98.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/3v4x ftp://data.pdbj.org/pub/pdb/validation_reports/v4/3v4x | HTTPS FTP |
-Related structure data
Related structure data | 3v4nC 1x9eS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 42596.934 Da / Num. of mol.: 4 / Mutation: A163S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 4200 / Gene: mvaS / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9FD71, hydroxymethylglutaryl-CoA synthase #2: Chemical | ChemComp-F24 / ( #3: Water | ChemComp-HOH / | |
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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: 1.94 Å3/Da / Density % sol: 36.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 23% PEG 3350, 0.2M NaCl, 0.1M Bis-Tris pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2011 |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.02 Å / Num. all: 96022 / Num. obs: 92978 / % possible obs: 96.8 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 4.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X9E Resolution: 1.952→48.02 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 21.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.37 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.952→48.02 Å
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Refine LS restraints |
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LS refinement shell |
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