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Yorodumi- PDB-5jvb: 1.95A resolution structure of PtxB from Trichodesmium erythraeum ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jvb | ||||||
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Title | 1.95A resolution structure of PtxB from Trichodesmium erythraeum IMS101 in complex with phosphite | ||||||
Components | Phosphonate ABC transporter, periplasmic phosphonate-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / periplasmic binding protein (PBP) / phosphite transpoter / cyanobacteria | ||||||
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. / PHOSPHONATE / Phosphonate ABC transporter, periplasmic phosphonate-binding protein Function and homology information | ||||||
Biological species | Trichodesmium erythraeum | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Bisson, C. / Adams, N.B.P. / Polyviou, D. / Bibby, T.S. / Hunter, C.N. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jvb.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jvb.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/5jvb ftp://data.pdbj.org/pub/pdb/validation_reports/jv/5jvb | HTTPS FTP |
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-Related structure data
Related structure data | 5lq1C 5lq5C 5lq8C 5lv1C 5me4C 5o2jC 5o2kC 5o37C 3p7iS 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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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 Source: (gene. exp.) Trichodesmium erythraeum (strain IMS101) (bacteria) Strain: IMS101 / Gene: Tery_0366 / Production host: Escherichia coli (E. coli) / References: UniProt: Q119I9 #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: 2.01 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.2 M NaCl, 0.1 M phosphate-citrate buffer pH 4.2 and 20 % PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→47.96 Å / Num. obs: 35004 / % possible obs: 97.2 % / Redundancy: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.3 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P7I Resolution: 1.95→47.96 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.27 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.185 / 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: 42.988 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→47.96 Å
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Refine LS restraints |
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