[English] 日本語
Yorodumi- PDB-5o37: Pseudomonas stutzeri PtxB in complex with methylphosphonate (MPn)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o37 | ||||||
---|---|---|---|---|---|---|---|
Title | Pseudomonas stutzeri PtxB in complex with methylphosphonate (MPn) to 1.37 A resolution | ||||||
Components | Probable phosphite transport system-binding protein PtxB | ||||||
Keywords | TRANSPORT PROTEIN / phosphite / ABC transporters / marine bacteria / PBP / SBP | ||||||
Function / homology | Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / ATP-binding cassette (ABC) transporter complex / transmembrane transport / METHYLPHOSPHONIC ACID ESTER GROUP / Probable phosphite transport system-binding protein PtxB Function and homology information | ||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Bisson, C. / Hitchcock, A. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: The molecular basis of phosphite and hypophosphite recognition by ABC-transporters. Authors: Bisson, C. / Adams, N.B.P. / Stevenson, B. / Brindley, A.A. / Polyviou, D. / Bibby, T.S. / Baker, P.J. / Hunter, C.N. / Hitchcock, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5o37.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5o37.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 5o37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/5o37 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/5o37 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5jvbC 5lq1C 5lq5C 5lq8C 5lv1C 5me4C 5o2jC 5o2kC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 30173.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal 6x His-tag / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: ptxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69052 |
---|---|
#2: Chemical | ChemComp-GB / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.92 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M MMT buffer pH 4 and 25 % (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→37.61 Å / Num. obs: 59851 / % possible obs: 99.9 % / Redundancy: 11.2 % / CC1/2: 1 / Rpim(I) all: 0.022 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.37→1.39 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2940 / CC1/2: 0.485 / Rpim(I) all: 0.615 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→37.61 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.75 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.115 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.37→37.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|