[English] 日本語
Yorodumi- PDB-6qbi: NMR structure of BB_P28, Borrelia burgdorferi outer surface lipop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qbi | ||||||
---|---|---|---|---|---|---|---|
Title | NMR structure of BB_P28, Borrelia burgdorferi outer surface lipoprotein | ||||||
Components | Surface protein, mlp lipoprotein family | ||||||
Keywords | MEMBRANE PROTEIN / Lipoprotein | ||||||
Function / homology | Mlp lipoprotein / Mlp lipoprotein family / cell outer membrane / Lipoprotein MlpA Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Fridmanis, J. / Otikovs, M. / Brangulis, K. / Jaudzems, K. | ||||||
Citation | Journal: Proteins / Year: 2020 Title: Solution NMR structure of Borrelia burgdorferi outer surface lipoprotein BBP28, a member of the mlp protein family. Authors: Fridmanis, J. / Otikovs, M. / Brangulis, K. / Tars, K. / Jaudzems, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6qbi.cif.gz | 584.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6qbi.ent.gz | 493.1 KB | Display | PDB format |
PDBx/mmJSON format | 6qbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qbi_validation.pdf.gz | 458.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6qbi_full_validation.pdf.gz | 633.7 KB | Display | |
Data in XML | 6qbi_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 6qbi_validation.cif.gz | 63.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/6qbi ftp://data.pdbj.org/pub/pdb/validation_reports/qb/6qbi | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 11038.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria) Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: mlpA, BB_P28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H7C7P1 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Type: solution Contents: 20 mM sodium phosphate, 50 mM sodium chloride, 0.03 % w/v sodium azide, 1 mM EDTA, 2 mM U-C13, N15 BB_P28, 93% H2O/7% D2O Label: BBP28_C13_N15 / Solvent system: 93% H2O/7% D2O | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||
Sample conditions | Ionic strength: 0.08 M / Ionic strength err: 0.01 / Label: Standart / pH: 6.8 / PH err: 0.1 / Pressure: AMBIENT Pa / Temperature: 298 K / Temperature err: 0.1 |
-NMR measurement
NMR spectrometer | Type: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |