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Yorodumi- PDB-5lv1: 2.12 A resolution structure of PtxB from Prochlorococcus marinus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lv1 | |||||||||||||||
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Title | 2.12 A resolution structure of PtxB from Prochlorococcus marinus (MIT 9301) in complex with phosphite | |||||||||||||||
Components | PtxB | |||||||||||||||
Keywords | PERIPLASMIC BINDING PROTEIN / ABC-transporter / phosphite / Prochlorococcus | |||||||||||||||
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / oxidanylphosphinate / Probable ABC transporter phosphonate/phosphite binding protein PhnD2 Function and homology information | |||||||||||||||
Biological species | Prochlorococcus marinus (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | |||||||||||||||
Authors | Bisson, C. / Adams, N.B.P. / Polyviou, D. / Bibby, T.S. / Hunter, C.N. / Hitchcock, A. | |||||||||||||||
Funding support | United Kingdom, 4items
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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 | 5lv1.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lv1.ent.gz | 127.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lv1_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 5lv1_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 5lv1_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 5lv1_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/5lv1 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/5lv1 | HTTPS FTP |
-Related structure data
Related structure data | 5jvbSC 5lq1C 5lq5C 5lq8C 5me4C 5o2jC 5o2kC 5o37C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30331.408 Da / Num. of mol.: 3 / Fragment: UNP residues 22-292 Source method: isolated from a genetically manipulated source Details: Truncated at the N-terminus to remove a signal peptide. C-terminal His-tag Source: (gene. exp.) Prochlorococcus marinus (strain MIT 9301) (bacteria) Gene: P9301_12511 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3PDP9 #2: Chemical | #3: 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: 2.49 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M Magnesium chloride, 0.1 M sodium citrate pH 5.0 and 15 % PEG 4000 |
-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 PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2016 |
Radiation | Monochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→131.79 Å / Num. obs: 51504 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.12→2.16 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.648 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JVB Resolution: 2.12→131.79 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.79 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.202 / 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: 30.215 Å2
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Refinement step | Cycle: 1 / Resolution: 2.12→131.79 Å
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