+Open data
-Basic information
Entry | Database: PDB / ID: 7fcf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of T6SS Hcp protein | ||||||
Components | (Fimbrial protein) x 2 | ||||||
Keywords | STRUCTURAL PROTEIN / Hexamer | ||||||
Function / homology | Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Fimbrial protein Function and homology information | ||||||
Biological species | Chromobacterium haemolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Jobichen, C. / Sivaraman, J. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Res.Microbiol. / Year: 2022 Title: Bacterial antagonism of Chromobacterium haemolyticum and characterization of its putative type VI secretion system. Authors: Zwe, Y.H. / Yadav, M. / Ten, M.M.Z. / Srinivasan, M. / Jobichen, C. / Sivaraman, J. / Li, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7fcf.cif.gz | 335.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7fcf.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7fcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/7fcf ftp://data.pdbj.org/pub/pdb/validation_reports/fc/7fcf | HTTPS FTP |
---|
-Related structure data
Related structure data | 1y12S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16771.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium haemolyticum (bacteria) Gene: B0T39_16745 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1W0CP47 |
---|---|
#2: Protein | Mass: 17785.938 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium haemolyticum (bacteria) Gene: B0T39_16745 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1W0CP47 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.99 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2M Ammonium acetate, 0.1M HEPES pH 7.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→46.41 Å / Num. obs: 15808 / % possible obs: 97.17 % / Redundancy: 10.6 % / Biso Wilson estimate: 153.62 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 22.75 |
Reflection shell | Resolution: 3.3→3.42 Å / Rmerge(I) obs: 1.31 / Num. unique obs: 1191 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y12 Resolution: 3.3→46.41 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.42 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→46.41 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|