+Open data
-Basic information
Entry | Database: PDB / ID: 8ovn | ||||||
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Title | X-ray structure of the SF-iGluSnFR-S72A | ||||||
Components | Putative periplasmic binding transport protein,Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / aspartate / genetically-encoded biosensor / iAspSnFR / GFP | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / outer membrane-bounded periplasmic space / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tarnawski, M. / Hellweg, L. / Bergner, A. / Hiblot, J. / Leippe, P. / Johnsson, K. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: X-ray structure of the SF-iGluSnFR-S72A Authors: Tarnawski, M. / Hellweg, L. / Bergner, A. / Hiblot, J. / Leippe, P. / Johnsson, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ovn.cif.gz | 133.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ovn.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 8ovn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/8ovn ftp://data.pdbj.org/pub/pdb/validation_reports/ov/8ovn | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58015.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ybeJ, SF0626, GFP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UXX1, UniProt: P42212 |
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#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 1.5 M tri-sodium citrate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00007 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 16, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00007 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 22091 / % possible obs: 99.9 % / Redundancy: 8.4 % / Biso Wilson estimate: 51.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2344 / CC1/2: 0.858 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.6 Å / SU ML: 0.3974 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.1484 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→46.6 Å
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Refine LS restraints |
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LS refinement shell |
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