+Open data
-Basic information
Entry | Database: PDB / ID: 6d21 | ||||||||||||
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Title | Crystal structure of the FERM domain of zebrafish FARP2 | ||||||||||||
Components | FERM, RhoGEF and pleckstrin domain protein 2 | ||||||||||||
Keywords | SIGNALING PROTEIN / membrane targeting | ||||||||||||
Function / homology | Function and homology information : / cytoskeletal protein binding / guanyl-nucleotide exchange factor activity / cytoskeleton Similarity search - Function | ||||||||||||
Biological species | Danio rerio (zebrafish) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å | ||||||||||||
Authors | Kuo, Y.C. / Zhang, X. | ||||||||||||
Funding support | United States, China, 3items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d21.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d21.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 6d21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/6d21 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/6d21 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39293.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: farp2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E7FE33 |
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#2: 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: 1.79 Å3/Da / Density % sol: 31.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium sodium tartrate tetrahydrate and 20 % PEG3350 (w/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.53 Å / Num. obs: 18882 / % possible obs: 98.6 % / Redundancy: 7.2 % / Net I/σ(I): 22.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→32.527 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.86 / 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: 1.999→32.527 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -12.2549 Å / Origin y: 2.5042 Å / Origin z: -9.2361 Å
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Refinement TLS group | Selection details: chain A |