[English] 日本語
Yorodumi- PDB-3d3n: Crystal structure of lipase/esterase (lp_2923) from Lactobacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d3n | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of lipase/esterase (lp_2923) from Lactobacillus plantarum. Northeast Structural Genomics Consortium target LpR108 | ||||||
Components | Putative lipase/esterase | ||||||
Keywords | HYDROLASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus plantarum WCFS1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Forouhar, F. / Su, M. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Foote, E.L. / Zhao, L. ...Forouhar, F. / Su, M. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Foote, E.L. / Zhao, L. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of lipase/esterase (lp_2923) from Lactobacillus plantarum. Northeast Structural Genomics Consortium target LpR108 Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Foote, E.L. / Zhao, L. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3d3n.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3d3n.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 3d3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/3d3n ftp://data.pdbj.org/pub/pdb/validation_reports/d3/3d3n | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31798.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria) Strain: WCFS1 / NCIMB 8826 / Gene: lp_2923, Aes / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q88TL9, UniProt: F9US10*PLUS #2: Chemical | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.84 % Description: The structure factor file contains Friedel pairs |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 5% PEG 8000, 100mM Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 38826 / Num. obs: 38826 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.07 / Net I/σ(I): 11.53 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.21 / Num. unique all: 3963 / Rsym value: 0.292 / % possible all: 98.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.5→19.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 425997.16 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: The Friedel pairs were used in phasing. Program XtalView has also been used in refinement
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.7578 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
|