[English] 日本語
Yorodumi- PDB-1j00: E. coli Thioesterase I/Protease I/Lysophospholipase L1 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j00 | ||||||
---|---|---|---|---|---|---|---|
Title | E. coli Thioesterase I/Protease I/Lysophospholipase L1 in complexed with diethyl phosphono moiety | ||||||
Components | Thioesterase I | ||||||
Keywords | HYDROLASE / Protease | ||||||
Function / homology | Function and homology information : / : / 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 / : / fatty acyl-CoA hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lo, Y.-C. / Shaw, J.-F. / Liaw, Y.-C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1j00.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1j00.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/1j00 ftp://data.pdbj.org/pub/pdb/validation_reports/j0/1j00 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ivnC 1jrlSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21697.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tesA/apeA/pldC / Plasmid: pET-20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P29679, UniProt: P0ADA1*PLUS, Hydrolases; Acting on ester bonds; Thioester hydrolases, lysophospholipase |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.1 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2-[N-morpholino]ethanesulfonic acid, PEGMME5000, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 133 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.12714 Å |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE |
Radiation | Monochromator: Si111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12714 Å / Relative weight: 1 |
Reflection | Resolution: 2→27.27 Å / Num. all: 15230 / Num. obs: 14582 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 28.3 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 17 / Limit k min: 0 / Limit l max: 85 / Limit l min: 0 / Observed criterion F max: 1788436.9 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 5.2 / % possible all: 98.9 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. obs: 15230 / % possible obs: 97.7 % / Rmerge(I) obs: 0.06 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JRL Resolution: 2→27.27 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 43.3515 Å2 / ksol: 0.354238 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.88 Å2 / Biso mean: 51.1 Å2 / Biso min: 23.13 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→27.27 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.237 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 2.07 Å |