+Open data
-Basic information
Entry | Database: PDB / ID: 6ghj | |||||||||
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Title | PepTSt in complex with tripeptide Phe-Ala-Gln | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / MFS / POT / peptide transporter | |||||||||
Function / homology | Function and homology information oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Streptococcus thermophilus (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | |||||||||
Authors | Martinez Molledo, M. / Quistgaard, E.M. / Loew, C. | |||||||||
Funding support | 2items
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Citation | Journal: FEBS Lett. / Year: 2018 Title: Tripeptide binding in a proton-dependent oligopeptide transporter. Authors: Martinez Molledo, M. / Quistgaard, E.M. / Low, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ghj.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ghj.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ghj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/6ghj ftp://data.pdbj.org/pub/pdb/validation_reports/gh/6ghj | HTTPS FTP |
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-Related structure data
Related structure data | 5oxoS S: Starting model for refinement |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 52782.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria) Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q5M4H8 |
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#2: Protein/peptide | Mass: 364.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-Non-polymers , 7 types, 121 molecules
#3: Chemical | #4: Chemical | ChemComp-1PE / | #5: Chemical | ChemComp-EPE / | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-78N / ( #8: Chemical | #9: 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: 2.88 Å3/Da / Density % sol: 57.36 % |
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Crystal grow | Temperature: 292.15 K / Method: lipidic cubic phase Details: 0.1-0.3 M HEPES buffer pH 7.5, 250 mM ammonium phosphate monobasic (NH4H2PO4), PEG400 (15-25%) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9143 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9143 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→48.69 Å / Num. obs: 29604 / % possible obs: 99.73 % / Redundancy: 10.3 % / Biso Wilson estimate: 40.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.44 |
Reflection shell | Resolution: 2.26→2.341 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.19 / CC1/2: 0.871 / % possible all: 99.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OXO Resolution: 2.26→48.69 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→48.69 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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