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- PDB-1ysl: Crystal structure of HMG-CoA synthase from Enterococcus faecalis ... -
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Open data
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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. | ||||||
![]() | (HMG-CoA synthase) x 2 | ||||||
![]() | LYASE / Thiolase family / CoEnzymeA | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Steussy, C.N. / Vartia, A.A. / Burgner II, J.W. / Sutherlin, A. / Rodwell, V.W. / Stauffacher, C.V. | ||||||
![]() | ![]() 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). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.2 KB | Display | ![]() |
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PDB format | ![]() | 137.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 768.8 KB | Display | ![]() |
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Full document | ![]() | 787 KB | Display | |
Data in XML | ![]() | 37.4 KB | Display | |
Data in CIF | ![]() | 53.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1x9eSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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. |
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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.) ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() ![]() References: GenBank: 9937383, UniProt: Q9FD71*PLUS, EC: 4.1.3.5 |
-Non-polymers , 5 types, 528 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/AAE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/AAE.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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