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Open data
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Basic information
Entry | Database: PDB / ID: 7kdc | ||||||
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Title | The complex between RhoD and the Plexin B2 RBD | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuo, Y. / Wang, Y. / Zhang, x. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A putative structural mechanism underlying the antithetic effect of homologous RND1 and RhoD GTPases in mammalian plexin regulation. Authors: Liu, Y. / Ke, P. / Kuo, Y.C. / Wang, Y. / Zhang, X. / Song, C. / Shan, Y. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 283.2 KB | Display | ![]() |
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PDB format | ![]() | 200.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 906.6 KB | Display | ![]() |
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Full document | ![]() | 917.1 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rexS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21335.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 11667.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | Sequence details | The original sequence for chains C and D included residues 1274 to 1842 of UNP PLXB2_MOUSE B2RXS4, ...The original sequence for chains C and D included residues 1274 to 1842 of UNP PLXB2_MOUSE B2RXS4, however, proteolytic cleavage occurs during incubation at an unknown site. Thus, the reported sequence corresponds to the portion observed in the coordinates, which is residues 1463 to 1565 of UNP PLXB2_MOUSE B2RXS4. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70.01 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion Details: 0.2 M MgCl2, 22 % (w/v) PEG 3350, and 100 mM MIB (pH 6.8, sodium malonate, imidazole, and boric acid mixed at 2:3:3 molar ratio). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.1→50 Å / Num. obs: 19325 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 107.05 Å2 / Rpim(I) all: 0.059 / Rsym value: 0.075 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 3.1→3.15 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 857 / CC1/2: 0.843 / Rpim(I) all: 0.465 / Rsym value: 0.514 / % possible all: 91.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2REX Resolution: 3.1→39.63 Å / SU ML: 0.4476 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 37.7234 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: 123.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→39.63 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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