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- PDB-3gvd: Crystal Structure of Serine Acetyltransferase CysE from Yersinia ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gvd | ||||||
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Title | Crystal Structure of Serine Acetyltransferase CysE from Yersinia pestis | ||||||
![]() | Serine acetyltransferase | ||||||
![]() | TRANSFERASE / left-handed beta-helix / Structural Genomics of National Institute of Allergy and Infectious Diseases / Acyltransferase / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Zhou, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Crystal Structure of Serine Acetyltransferase CysE from Yersinia pestis Authors: Kim, Y. / Zhou, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 976.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1t3dS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 29478.680 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: N-terminal His-tag with TEV cleavage site / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q0WKM4, UniProt: A0A2U2H3H7*PLUS, serine O-acetyltransferase |
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-Non-polymers , 7 types, 1043 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG5.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG5.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACY / #4: Chemical | ChemComp-CYS / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PG5 / | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M Potassium acetate, 20% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2009 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.17 Å / Num. all: 112894 / Num. obs: 112894 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 32.44 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.2 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1T3D Resolution: 2.4→45.986 Å / SU ML: 0.39 / Isotropic thermal model: isotropic / σ(F): 1.96 / Phase error: 32.35 / 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: 31.29 Å2 / ksol: 0.309 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→45.986 Å
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Refine LS restraints |
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LS refinement shell |
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