[English] 日本語
Yorodumi- PDB-7tpm: Structure of the outer-membrane lipoprotein carrier protein (LolA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tpm | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the outer-membrane lipoprotein carrier protein (LolA) from Borrelia burgdorferi | ||||||
Components | Outer membrane lipoprotein carrier protein LolA | ||||||
Keywords | LIPID TRANSPORT / lipoprotein carrier protein / LolA / Borreliella burgdorferi / Lyme disease spirochete | ||||||
Function / homology | Outer membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / Export chaperone Function and homology information | ||||||
Biological species | Borreliella burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / Resolution: 1.9 Å | ||||||
Authors | Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Zueckert, W.R. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To be published Title: Structure of the outer-membrane lipoprotein carrier protein (LolA) from Borrelia burgdorferi Authors: Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Zueckert, W.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7tpm.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7tpm.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 7tpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tpm_validation.pdf.gz | 682.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7tpm_full_validation.pdf.gz | 683 KB | Display | |
Data in XML | 7tpm_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 7tpm_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/7tpm ftp://data.pdbj.org/pub/pdb/validation_reports/tp/7tpm | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23403.543 Da / Num. of mol.: 1 / Fragment: Q18-N216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Gene: BB_0346 / Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: O51321 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-PE4 / | ||||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.08 % / Mosaicity: 0.04 ° |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2 M sodium formate, 100 mM MES, 5% (w/v) PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→49.86 Å / Num. obs: 25182 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 33.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Net I/σ(I): 12.5 / Num. measured all: 488064 / Scaling rejects: 1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: SAD |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAD-phased structure of the same protein from a KI-soaked crystal Resolution: 1.9→38.623 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.06 / Phase error: 24.52 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.69 Å2 / Biso mean: 37.2703 Å2 / Biso min: 20.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→38.623 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
|