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Yorodumi- PDB-5lq8: 1.52 A resolution structure of PhnD1 from Prochlorococcus marinus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lq8 | |||||||||||||||
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Title | 1.52 A resolution structure of PhnD1 from Prochlorococcus marinus (MIT 9301) in complex with methylphosphonate | |||||||||||||||
Components | Putative phosphonate binding protein for ABC transporter | |||||||||||||||
Keywords | PERIPLASMIC BINDING PROTEIN / ABC-transporter / methylphosphonate / Prochlorococcus | |||||||||||||||
Function / homology | Putative ABC transporter periplasmic binding protein PhnD-like / Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / METHYLPHOSPHONIC ACID ESTER GROUP / Probable ABC transporter phosphite binding protein PhnD1 Function and homology information | |||||||||||||||
Biological species | Prochlorococcus marinus str. MIT 9301 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 | 5lq8.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lq8.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lq8_validation.pdf.gz | 428.7 KB | Display | wwPDB validaton report |
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Full document | 5lq8_full_validation.pdf.gz | 429.5 KB | Display | |
Data in XML | 5lq8_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 5lq8_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/5lq8 ftp://data.pdbj.org/pub/pdb/validation_reports/lq/5lq8 | HTTPS FTP |
-Related structure data
Related structure data | 5jvbC 5lq1C 5lq5SC 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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Unit cell |
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-Components
#1: Protein | Mass: 32329.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The construct is truncated by 24 residues at the N-terminus to remove a signal peptide and has a C-terminal 6XHis tag. Source: (gene. exp.) Prochlorococcus marinus str. MIT 9301 (bacteria) Gene: phnD, P9301_07261 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3PC74 | ||
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#2: Chemical | #3: 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: 2.1 Å3/Da / Density % sol: 41.49 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M MMT (DL-malic acid, MES and Tris base) buffer pH 8.0 and 25% (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97951 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→44 Å / Num. obs: 40089 / % possible obs: 97 % / Redundancy: 2.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.021 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.679 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LQ5 Resolution: 1.52→44 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.481 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.079 / 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: 37.022 Å2
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Refinement step | Cycle: 1 / Resolution: 1.52→44 Å
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Refine LS restraints |
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