+Open data
-Basic information
Entry | Database: PDB / ID: 5oxq | ||||||
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Title | PepTSt in complex with HEPES (300 mM) | ||||||
Components | Di-or tripeptide:H+ symporter | ||||||
Keywords | TRANSPORT PROTEIN / Alpha-helical membrane protein / membrane protein / MFS fold / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 Å | ||||||
Authors | Martinez Molledo, M. / Quistgaard, E.M. / Loew, C. | ||||||
Citation | Journal: Structure / Year: 2018 Title: Multispecific Substrate Recognition in a Proton-Dependent Oligopeptide Transporter. Authors: Martinez Molledo, M. / Quistgaard, E.M. / Flayhan, A. / Pieprzyk, J. / Low, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oxq.cif.gz | 205 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oxq.ent.gz | 165 KB | Display | PDB format |
PDBx/mmJSON format | 5oxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/5oxq ftp://data.pdbj.org/pub/pdb/validation_reports/ox/5oxq | HTTPS FTP |
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-Related structure data
Related structure data | 5oxkC 5oxlC 5oxmC 5oxnC 5oxoC 5oxpC 6eiaC 4d2dS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53648.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: dtpT, stu0970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q5M4H8 |
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-Non-polymers , 7 types, 124 molecules
#2: Chemical | ChemComp-NA / | ||||||||||
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#3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-1PE / | #5: Chemical | #6: Chemical | ChemComp-78N / ( #7: Chemical | ChemComp-78M / ( #8: 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: 2.87 Å3/Da / Density % sol: 57.14 % |
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Crystal grow | Temperature: 292.15 K / Method: lipidic cubic phase Details: 0.3 M HEPES pH 7.0, 0.25 M ammonium phosphate monobasic, 21% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.195→46.31 Å / Num. obs: 31840 / % possible obs: 99.68 % / Redundancy: 13.1 % / Biso Wilson estimate: 45.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1321 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.195→2.274 Å / Redundancy: 12 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 3090 / CC1/2: 0.408 / % possible all: 97.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D2D Resolution: 2.195→46.31 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.195→46.31 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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