+Open data
-Basic information
Entry | Database: PDB / ID: 6fms | ||||||||||||
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Title | IMISX-EP of Se-LspA | ||||||||||||
Components |
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Keywords | HYDROLASE / Serial crystallography / experimental phasing / in meso crystallization / in situ diffraction data collection / membrane protein structure / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information signal peptidase II / signal peptide processing / aspartic-type endopeptidase activity / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 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 | 6fms.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fms.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/6fms ftp://data.pdbj.org/pub/pdb/validation_reports/fm/6fms | HTTPS FTP |
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-Related structure data
Related structure data | 6fmrC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 21287.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Gene: lspA, ls, PA4559 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HVM5, signal peptidase II #2: Protein/peptide | #3: Chemical | ChemComp-OLC / ( #4: 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: 3.78 Å3/Da / Density % sol: 67.49 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 35 % PEG 400, 100 mM MES, pH 5.6, and 100 mM ammonium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97858 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97858 Å / Relative weight: 1 |
Reflection | Resolution: 3→46.27 Å / Num. obs: 41032 / % possible obs: 99.9 % / Redundancy: 22.7 % / CC1/2: 0.99 / Rrim(I) all: 0.31 / Net I/σ(I): 9.14 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 22.7 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 3031 / CC1/2: 0.4 / Rrim(I) all: 3.46 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→46.268 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 3→46.268 Å
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