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Yorodumi- PDB-5o2j: Pseudomonas stutzeri PtxB in complex with phosphite to 1.52 A res... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o2j | ||||||||||||||||||
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Title | Pseudomonas stutzeri PtxB in complex with phosphite to 1.52 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 / PHOSPHONATE / Probable phosphite transport system-binding protein PtxB Function and homology information | ||||||||||||||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||||||||||||||
Authors | Bisson, C. / Hitchcock, A. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o2j.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o2j.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 5o2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o2j_validation.pdf.gz | 432.9 KB | Display | wwPDB validaton report |
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Full document | 5o2j_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 5o2j_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 5o2j_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/5o2j ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o2j | HTTPS FTP |
-Related structure data
Related structure data | 5jvbC 5lq1C 5lq5C 5lq8C 5lv1C 5me4C 5o2kC 5o37C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30173.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 6x His-tag at C-terminus / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: ptxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69052 |
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#2: Chemical | ChemComp-2PO / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.11 % / Description: rods |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MMT buffer pH 5 25% (w/v) and PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: 1.52→33.25 Å / Num. obs: 44234 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rpim(I) all: 0.039 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2169 / CC1/2: 0.51 / Rpim(I) all: 0.607 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→33.25 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.252 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.051 Å2
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Refinement step | Cycle: 1 / Resolution: 1.52→33.25 Å
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Refine LS restraints |
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