+Open data
-Basic information
Entry | Database: PDB / ID: 6d2q | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the FERM domain of zebrafish FARP1 | ||||||||||||
Components | FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived) | ||||||||||||
Keywords | SIGNALING PROTEIN / membrane targeting | ||||||||||||
Function / homology | Function and homology information phosphatidylinositol phosphate binding / glomerular filtration / phosphatidylserine binding / cytoskeletal protein binding / phosphatidylinositol binding / guanyl-nucleotide exchange factor activity / cytoskeleton Similarity search - Function | ||||||||||||
Biological species | Danio rerio (zebrafish) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||||||||
Authors | Kuo, Y.C. / Zhang, X. | ||||||||||||
Funding support | United States, China, 3items
| ||||||||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Structural analyses of FERM domain-mediated membrane localization of FARP1. Authors: Kuo, Y.C. / He, X. / Coleman, A.J. / Chen, Y.J. / Dasari, P. / Liou, J. / Biederer, T. / Zhang, X. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6d2q.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6d2q.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 6d2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/6d2q ftp://data.pdbj.org/pub/pdb/validation_reports/d2/6d2q | HTTPS FTP |
---|
-Related structure data
Related structure data | 6d21C 6d2kSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33361.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: farp1, si:ch211-235f1.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9QIC8 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.43 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine pH 9.0, 16 % MPD (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→40.77 Å / Num. obs: 6910 / % possible obs: 99.34 % / Redundancy: 11.6 % / Net I/σ(I): 12.75 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6D2K Resolution: 2.99→40.77 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.35
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.99→40.77 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 14.1915 Å / Origin y: 2.6237 Å / Origin z: 12.8098 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: chain A |