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Open data
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Basic information
Entry | Database: PDB / ID: 3doh | ||||||
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Title | Crystal Structure of a Thermostable Esterase | ||||||
![]() | esterase | ||||||
![]() | HYDROLASE / alpha-beta Hydrolase / beta sheet | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Levisson, M. / Sun, L. / Hendriks, S. / Dijkstra, B.W. / Van der Oost, J. / Kengen, S.W.M. | ||||||
![]() | ![]() Title: Crystal structure and biochemical properties of a novel thermostable esterase containing an immunoglobulin-like domain. Authors: Levisson, M. / Sun, L. / Hendriks, S. / Swinkels, P. / Akveld, T. / Bultema, J.B. / Barendregt, A. / van den Heuvel, R.H.H. / Dijkstra, B.W. / van der Oost, J. / Kengen, S.W.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.7 KB | Display | ![]() |
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PDB format | ![]() | 129.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.2 KB | Display | ![]() |
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Full document | ![]() | 487.9 KB | Display | |
Data in XML | ![]() | 32.2 KB | Display | |
Data in CIF | ![]() | 44.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43067.750 Da / Num. of mol.: 2 / Fragment: residues 16-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 8000, 1M lithium sulphate monohydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2007 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→50 Å / Num. obs: 31079 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.2 | |||||||||||||||
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.122 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20
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