[English] 日本語
![](img/lk-miru.gif)
- PDB-8dc1: Structural and biochemical characterization of L. interrogans Lsa... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8dc1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structural and biochemical characterization of L. interrogans Lsa45 reveals a penicillin-binding protein with esterase activity | |||||||||
![]() | Lsa45 | |||||||||
![]() | HYDROLASE / Leptospira / esterase / PBP / Beta-Lactamase | |||||||||
Function / homology | Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / IODIDE ION / DI(HYDROXYETHYL)ETHER / Putative lipoprotein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Santos, J.C. / Nascimento, A.L.T.O. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural and biochemical characterization of Leptospira interrogans Lsa45 reveals a penicillin-binding protein with esterase activity. Authors: Santos, J.C. / Handa, S. / Fernandes, L.G.V. / Bleicher, L. / Gandin, C.A. / de Oliveira-Neto, M. / Ghosh, P. / Nascimento, A.L.T.O. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 155.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 120.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 4.8 MB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38828.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Fiocruz L1-130 / Gene: LIC_10731 / Production host: ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-PEG / | ||||||
#3: Chemical | ChemComp-IOD / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.11 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Solution consisting of 100 mM Tris-HCl, pH 8.5, 30% PEG 1500 and 8% MPD |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 15, 2018 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5499 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→45.22 Å / Num. obs: 48588 / % possible obs: 99.7 % / Redundancy: 31.5 % / Biso Wilson estimate: 17.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.033 / Rrim(I) all: 0.184 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 20.9 % / Rmerge(I) obs: 2.786 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2223 / CC1/2: 0.524 / Rpim(I) all: 0.619 / Rrim(I) all: 2.858 / % possible all: 94.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.489 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→41.17 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.62→1.662 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 5.354 Å / Origin y: 46.933 Å / Origin z: 81.809 Å
|