+Open data
-Basic information
Entry | Database: PDB / ID: 6fmr | |||||||||
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Title | IMISX-EP of Se-PepTSt | |||||||||
Components | Di-or tripeptide:H+ symporter | |||||||||
Keywords | TRANSPORT PROTEIN / Serial crystallography / experimental phasing / in meso crystallization / in situ diffraction data collection / membrane protein structure. | |||||||||
Function / homology | Function and homology information oligopeptide transport / peptide transmembrane transporter activity / peptide transport / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Streptococcus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | |||||||||
Authors | Huang, C.-Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M. | |||||||||
Funding support | Ireland, Switzerland, 2items
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Citation | Journal: Commun Biol / Year: 2018 Title: In situ serial crystallography for rapid de novo membrane protein structure determination. Authors: Huang, C.Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fmr.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fmr.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fmr_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 6fmr_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6fmr_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 6fmr_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/6fmr ftp://data.pdbj.org/pub/pdb/validation_reports/fm/6fmr | HTTPS FTP |
-Related structure data
Related structure data | 6fmsC 6fmtC 6fmvC 6fmwC 6fmxC 6fmyC 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: 53638.867 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) / References: UniProt: Q5M4H8 | ||||
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#2: Chemical | ChemComp-78M / ( #3: Chemical | ChemComp-PO4 / | #4: 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: 2.96 Å3/Da / Density % sol: 58.38 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7 Details: 22 %(v/v) PEG- 400, 325 mM ammonium dihydrogen phosphate, 100 mM HEPES, pH 7.0, and 10 mM cefadroxil |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97854 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97854 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.54 Å / Num. obs: 33746 / % possible obs: 100 % / Redundancy: 25.4 % / CC1/2: 0.99 / Rrim(I) all: 0.44 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 23.8 % / Mean I/σ(I) obs: 1.74 / Num. unique obs: 2460 / CC1/2: 0.45 / Rrim(I) all: 3.69 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→49.54 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.7→49.54 Å
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