[English] 日本語
Yorodumi- PDB-6v8q: Structure of an inner membrane protein required for PhoPQ regulat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v8q | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of an inner membrane protein required for PhoPQ regulated increases in outer membrane cardiolipin | |||||||||
Components | Inner membrane protein YejM | |||||||||
Keywords | MEMBRANE PROTEIN / PbgA / CL transport / PhoPQ / outer membrane barrier | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69958498172 Å | |||||||||
Authors | Fan, J. / Miller, S. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Mbio / Year: 2020 Title: Structure of an Inner Membrane Protein Required for PhoPQ-Regulated Increases in Outer Membrane Cardiolipin. Authors: Fan, J. / Petersen, E.M. / Hinds, T.R. / Zheng, N. / Miller, S.I. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6v8q.cif.gz | 532.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6v8q.ent.gz | 386.6 KB | Display | PDB format |
PDBx/mmJSON format | 6v8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v8q_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6v8q_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6v8q_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 6v8q_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/6v8q ftp://data.pdbj.org/pub/pdb/validation_reports/v8/6v8q | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 68053.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria) Gene: yejM, STM2228 / Production host: Escherichia coli (E. coli) / References: UniProt: P40709 #2: Chemical | ChemComp-CA / | #3: Chemical | #4: Chemical | ChemComp-QSR / ( #5: Sugar | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.81 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.4 M (NH4)2SO4, 0.1 M MES (pH 6.5), and 10% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→50 Å / Num. obs: 53782 / % possible obs: 97.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 53.9684885527 Å2 / Rpim(I) all: 0.086 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Num. unique obs: 763 / CC1/2: 0.31 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PbgA periplasmic domain Resolution: 2.69958498172→48.342488687 Å / SU ML: 0.37638269452 / Cross valid method: FREE R-VALUE / σ(F): 1.35423336696 / Phase error: 36.5142096275
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.3367581053 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.69958498172→48.342488687 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 140.315222582 Å / Origin y: -9.40515681879 Å / Origin z: 336.286619625 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |