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Open data
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Basic information
Entry | Database: PDB / ID: 1ivn | ||||||
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Title | E.coli Thioesterase I/Protease I/Lysophospholiase L1 | ||||||
![]() | Thioesterase I | ||||||
![]() | HYDROLASE / Protease | ||||||
Function / homology | ![]() : / : / : / arylesterase / : / phosphatidyl phospholipase B activity / lysophospholipase / : / palmitoyl-CoA hydrolase / fatty acyl-[ACP] hydrolase activity ...: / : / : / arylesterase / : / phosphatidyl phospholipase B activity / lysophospholipase / : / palmitoyl-CoA hydrolase / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-CoA hydrolase activity / lysophospholipase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / arylesterase activity / lipid metabolic process / peptidase activity / outer membrane-bounded periplasmic space / periplasmic space / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lo, Y.-C. / Shaw, J.-F. / Liaw, Y.-C. | ||||||
![]() | ![]() Title: Crystal Structure of Escherichia coli Thioesterase I/Protease I/Lysophospholipase L1: Consensus Sequence Blocks Constitute the Catalytic Center of SGNH-hydrolases through a Conserved Hydrogen Bond Network Authors: Lo, Y.-C. / Lin, S.-C. / Shaw, J.-F. / Liaw, Y.-C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.4 KB | Display | ![]() |
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PDB format | ![]() | 37.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.8 KB | Display | ![]() |
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Full document | ![]() | 453.1 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1j00C ![]() 1jrlSC ![]() 1nyv C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21561.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P29679, UniProt: P0ADA1*PLUS, lysophospholipase, Hydrolases; Acting on ester bonds; Thioester hydrolases |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.56 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2-[N-morpholino]ethanesulfonic acid, PEGMME 5000, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 133 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9236 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→28.15 Å / Num. all: 17352 / Num. obs: 17352 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.96 % / Biso Wilson estimate: 26.6 Å2 / Limit h max: 25 / Limit h min: 0 / Limit k max: 18 / Limit k min: 0 / Limit l max: 88 / Limit l min: 0 / Observed criterion F max: 706205.76 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 4.94 / % possible all: 87.2 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 28.1 Å / Num. obs: 17893 / Redundancy: 21 % |
Reflection shell | *PLUS Lowest resolution: 2 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JRL Resolution: 1.9→28.15 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 52.2166 Å2 / ksol: 0.383183 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.63 Å2 / Biso mean: 46.8 Å2 / Biso min: 22.55 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→28.15 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 28.1 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2 Å |