+Open data
-Basic information
Entry | Database: PDB / ID: 6fmt | |||||||||
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Title | IMISX-EP of Hg-BacA Soaking SAD | |||||||||
Components | Undecaprenyl-diphosphatase | |||||||||
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 undecaprenyl-diphosphate phosphatase / undecaprenyl-diphosphatase activity / pyrophosphatase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
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 | 6fmt.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fmt.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fmt_validation.pdf.gz | 978.9 KB | Display | wwPDB validaton report |
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Full document | 6fmt_full_validation.pdf.gz | 989.6 KB | Display | |
Data in XML | 6fmt_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 6fmt_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/6fmt ftp://data.pdbj.org/pub/pdb/validation_reports/fm/6fmt | HTTPS FTP |
-Related structure data
Related structure data | 6fmrC 6fmsC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30887.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: uppP, bacA, upk, b3057, JW3029 / Production host: Escherichia coli (E. coli) References: UniProt: P60932, UniProt: P60933*PLUS, undecaprenyl-diphosphate phosphatase | ||||
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#2: Chemical | ChemComp-HG / | ||||
#3: Chemical | ChemComp-OLC / ( #4: Chemical | ChemComp-TRS / | #5: 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: 2.68 Å3/Da / Density % sol: 54.09 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 40 % PEG-400, 0.3-0.5 M ammonium citrate dibasic and 0.1 M sodium citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.9 Å / Relative weight: 1 |
Reflection | Resolution: 3→44.58 Å / Num. obs: 12841 / % possible obs: 100 % / Redundancy: 65.4 % / Rrim(I) all: 0.48 / Net I/σ(I): 10.62 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 60.7 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 977 / Rrim(I) all: 3.93 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→44.558 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 3→44.558 Å
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