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Yorodumi- PDB-5o2k: Native apo-structure of Pseudomonas stutzeri PtxB to 2.1 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o2k | ||||||||||||||||||
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Title | Native apo-structure of Pseudomonas stutzeri PtxB to 2.1 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 / Probable phosphite transport system-binding protein PtxB Function and homology information | ||||||||||||||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 5o2k.cif.gz | 303.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o2k.ent.gz | 249.1 KB | Display | PDB format |
PDBx/mmJSON format | 5o2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o2k_validation.pdf.gz | 457.8 KB | Display | wwPDB validaton report |
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Full document | 5o2k_full_validation.pdf.gz | 461.4 KB | Display | |
Data in XML | 5o2k_validation.xml.gz | 53 KB | Display | |
Data in CIF | 5o2k_validation.cif.gz | 74.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/5o2k ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o2k | HTTPS FTP |
-Related structure data
Related structure data | 5jvbC 5lq1C 5lq5C 5lq8C 5lv1C 5me4C 5o2jC 5o37C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 30173.084 Da / Num. of mol.: 6 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.98 % / Description: rods |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M tri-sodium citrate pH 5.5 and 20 % (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→79.75 Å / Num. obs: 113030 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rpim(I) all: 0.078 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5565 / CC1/2: 0.535 / Rpim(I) all: 0.625 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→79.69 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.462 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.041 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→79.69 Å
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Refine LS restraints |
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