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Yorodumi- PDB-6gz9: Crystal structure of a POT family transporter in complex with pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gz9 | ||||||
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Title | Crystal structure of a POT family transporter in complex with prodrug valacyclovir | ||||||
Components | Peptide ABC transporter permease | ||||||
Keywords | MEMBRANE PROTEIN / Peptide transporter / prodrug complex | ||||||
Function / homology | Function and homology information peptide transmembrane transporter activity / peptide transport / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Staphylococcus hominis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Minhas, G.S. / Newstead, S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Structural basis for prodrug recognition by the SLC15 family of proton-coupled peptide transporters. Authors: Minhas, G.S. / Newstead, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gz9.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gz9.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 6gz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gz9_validation.pdf.gz | 667.3 KB | Display | wwPDB validaton report |
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Full document | 6gz9_full_validation.pdf.gz | 674.4 KB | Display | |
Data in XML | 6gz9_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 6gz9_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/6gz9 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/6gz9 | HTTPS FTP |
-Related structure data
Related structure data | 6h7uC 6hzpC 6exsS 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: 53951.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus hominis (bacteria) / Gene: BL313_09825 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: A0A1L8Y4Q3, UniProt: A0A657M1C3*PLUS |
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#2: Chemical | ChemComp-TXC / |
#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: 3.02 Å3/Da / Density % sol: 59.33 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5 Details: 26-27% (v/v) PEG 200, 220 mM (NH4)2HPO4, and 110 mM sodium citrate (pH 5.0). Ligand: 40mM valacyclovir |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.96861 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→58.2 Å / Num. obs: 11917 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 60.92 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.36 / Rpim(I) all: 0.23 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.17 / Num. unique obs: 2145 / CC1/2: 0.547 / Rpim(I) all: 0.94 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EXS Resolution: 3.1→58.162 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.79 Å2 / Biso mean: 69.1491 Å2 / Biso min: 33.95 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→58.162 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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