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Yorodumi- PDB-1ysl: Crystal structure of HMG-CoA synthase from Enterococcus faecalis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ysl | ||||||
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Title | Crystal structure of HMG-CoA synthase from Enterococcus faecalis with AcetoAcetyl-CoA ligand. | ||||||
Components | (HMG-CoA synthaseHydroxymethylglutaryl-CoA synthase) x 2 | ||||||
Keywords | LYASE / Thiolase family / CoEnzymeA | ||||||
Function / homology | Function and homology information hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Steussy, C.N. / Vartia, A.A. / Burgner II, J.W. / Sutherlin, A. / Rodwell, V.W. / Stauffacher, C.V. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: X-ray Crystal Structures of HMG-CoA Synthase from Enterococcus faecalis and a Complex with Its Second Substrate/Inhibitor Acetoacetyl-CoA. Authors: Steussy, C.N. / Vartia, A.A. / Burgner II, J.W. / Sutherlin, A. / Rodwell, V.W. / Stauffacher, C.V. | ||||||
History |
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Remark 400 | COMPOUND THE ACETOACETYL MOLECULE, AAE IS COVALENTLY ATTACHED TO CYSTEINE B111 WITH 50% OCCUPANCY. ...COMPOUND THE ACETOACETYL MOLECULE, AAE IS COVALENTLY ATTACHED TO CYSTEINE B111 WITH 50% OCCUPANCY. THE REMAINING PORTION OF CYSTEINE B111 IS OXIDIZED TO SULFONATE (CSD). CYSTEINE A 111 IS ENTIRELY OXIDIZED (CSD). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ysl.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ysl.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ysl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/1ysl ftp://data.pdbj.org/pub/pdb/validation_reports/ys/1ysl | HTTPS FTP |
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-Related structure data
Related structure data | 1x9eSC 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 on special symmetry positions |
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Details | The asymmetric unit contains a homodimer that is believed to be the biologically active unit. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 44307.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] References: GenBank: 9937383, UniProt: Q9FD71*PLUS, EC: 4.1.3.5 |
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#2: Protein | Mass: 44275.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] References: GenBank: 9937383, UniProt: Q9FD71*PLUS, EC: 4.1.3.5 |
-Non-polymers , 5 types, 528 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-COA / | #6: Chemical | ChemComp-AAE / | #7: 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: 2.39 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 2.4M ammonium sulfate, 100 mM MES, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2004 / Details: Bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→28 Å / Num. all: 63975 / Num. obs: 63975 / % possible obs: 100 % / Observed criterion σ(F): 63975 / Observed criterion σ(I): 63975 |
Reflection shell | Resolution: 1.9→1.95 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1x9e Resolution: 1.9→28 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→28 Å
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Refine LS restraints |
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