+Open data
-Basic information
Entry | Database: PDB / ID: 6fmx | |||||||||
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Title | IMISX-EP of W-PgpB | |||||||||
Components | Phosphatidylglycerophosphatase B | |||||||||
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 phosphatidylglycerophosphatase / phosphatidylglycerophosphatase activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 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 | 6fmx.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fmx.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 6fmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fmx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6fmx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6fmx_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 6fmx_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/6fmx ftp://data.pdbj.org/pub/pdb/validation_reports/fm/6fmx | HTTPS FTP |
-Related structure data
Related structure data | 6fmrC 6fmsC 6fmtC 6fmvC 6fmwC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25155.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: pgpB, yodM, BSU19650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O34349, phosphatidylglycerophosphatase | ||||
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#2: Chemical | ChemComp-OLC / ( #3: Chemical | ChemComp-WO4 / | #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: 2.9 Å3/Da / Density % sol: 57.62 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 40 %(v/v) PEG-400, 100 mM HEPES pH 7 and 100 mM lithium citrate tribasic tetrahydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.21371 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.21371 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→35.614 Å / Num. obs: 39988 / % possible obs: 91.7 % / Redundancy: 2.6 % / CC1/2: 0.92 / Rrim(I) all: 0.1 / Net I/σ(I): 7.93 |
Reflection shell | Resolution: 1.79→1.9 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 0.91 / Num. unique obs: 6925 / CC1/2: 0.5 / Rrim(I) all: 1.32 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.79→35.614 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.85 / Phase error: 31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→35.614 Å
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Refine LS restraints |
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LS refinement shell |
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