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Yorodumi- PDB-5lq1: 1.41 A resolution structure of PtxB from Trichodesmium erythraeum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lq1 | |||||||||||||||
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Title | 1.41 A resolution structure of PtxB from Trichodesmium erythraeum IMS101 in complex with methylphosphonate | |||||||||||||||
Components | Phosphonate ABC transporter, periplasmic phosphonate-binding protein | |||||||||||||||
Keywords | TRANSPORT PROTEIN / ABC transporter / phosphite / methylphosphonate / periplasmic binding protein | |||||||||||||||
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. / METHYLPHOSPHONIC ACID ESTER GROUP / Phosphonate ABC transporter, periplasmic phosphonate-binding protein Function and homology information | |||||||||||||||
Biological species | Trichodesmium erythraeum IMS101 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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 | 5lq1.cif.gz | 222.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lq1.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/5lq1 ftp://data.pdbj.org/pub/pdb/validation_reports/lq/5lq1 | HTTPS FTP |
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-Related structure data
Related structure data | 5jvbSC 5lq5C 5lq8C 5lv1C 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31173.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The construct is truncated by 26 residues at the N-termius to remove a signal peptide. Source: (gene. exp.) Trichodesmium erythraeum IMS101 (bacteria) Gene: Tery_0366 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q119I9 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: 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: 2.15 Å3/Da / Density % sol: 42.71 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M Magnesium chloride, 0.1 M Sodium acetate pH 5.0 and 20 % (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97629 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→65.05 Å / Num. obs: 91920 / % possible obs: 95.2 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.41→1.43 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.48 / % possible all: 75.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JVB Resolution: 1.41→64.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.251 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.075 / 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: 26.361 Å2
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Refinement step | Cycle: 1 / Resolution: 1.41→64.98 Å
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Refine LS restraints |
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