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Yorodumi- PDB-2efk: Crystal structure of the EFC domain of Cdc42-interacting protein 4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2efk | ||||||
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Title | Crystal structure of the EFC domain of Cdc42-interacting protein 4 | ||||||
Components | Cdc42-interacting protein 4 | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / EFC domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information cell communication / phagocytic cup / RHOQ GTPase cycle / cell projection / endocytosis / Clathrin-mediated endocytosis / cell cortex / actin cytoskeleton organization / lysosome / cytoskeleton ...cell communication / phagocytic cup / RHOQ GTPase cycle / cell projection / endocytosis / Clathrin-mediated endocytosis / cell cortex / actin cytoskeleton organization / lysosome / cytoskeleton / intracellular membrane-bounded organelle / lipid binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Shimada, A. / Niwa, H. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2007 Title: Curved EFC/F-BAR-Domain Dimers Are Joined End to End into a Filament for Membrane Invagination in Endocytosis Authors: Shimada, A. / Niwa, H. / Tsujita, K. / Suetsugu, S. / Nitta, K. / Hanawa-Suetsugu, K. / Akasaka, R. / Nishino, Y. / Toyama, M. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Yamamoto, M. / Terada, ...Authors: Shimada, A. / Niwa, H. / Tsujita, K. / Suetsugu, S. / Nitta, K. / Hanawa-Suetsugu, K. / Akasaka, R. / Nishino, Y. / Toyama, M. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Yamamoto, M. / Terada, T. / Miyazawa, A. / Tanaka, A. / Sugano, S. / Shirouzu, M. / Nagayama, K. / Takenawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2efk.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2efk.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 2efk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2efk ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2efk | 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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Details | The second part of the biological assembly is generated by the two fold axis: -x, y, -z |
-Components
#1: Protein | Mass: 34970.078 Da / Num. of mol.: 1 / Fragment: EFC DOMAIN, residues 10-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / References: UniProt: Q15642 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.91 % |
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Crystal grow | Temperature: 277 K / Method: small tubes / pH: 8 Details: 20mM Tris-HCl, 150mM NaCl, 2mM DTT, pH 8.0, SMALL TUBES, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. all: 16924 / Num. obs: 16924 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.1 | ||||||||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1120 / % possible all: 61.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→45.29 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2725144.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.185 Å2 / ksol: 0.329316 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→45.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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