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- PDB-2xqn: Complex of the 2nd and 3rd LIM domains of TES with the EVH1 DOMAI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xqn | ||||||
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Title | Complex of the 2nd and 3rd LIM domains of TES with the EVH1 DOMAIN of MENA and the N-Terminal domain of actin-like protein Arp7A | ||||||
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![]() | METAL BINDING PROTEIN / METAL-BINDING PROTEIN / CYTOSKELETON / FOCAL ADHESION / ACROSOME | ||||||
Function / homology | ![]() actin polymerization-dependent cell motility / dynactin complex / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / motile cilium / Generation of second messenger molecules / filopodium / male germ cell nucleus ...actin polymerization-dependent cell motility / dynactin complex / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / motile cilium / Generation of second messenger molecules / filopodium / male germ cell nucleus / axon guidance / structural constituent of cytoskeleton / SH3 domain binding / actin cytoskeleton / lamellipodium / cell junction / actin binding / cytoskeleton / cadherin binding / negative regulation of cell population proliferation / focal adhesion / synapse / Golgi apparatus / protein-containing complex / RNA binding / zinc ion binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Knowles, P.P. / Briggs, D.C. / Murray-Rust, J. / McDonald, N.Q. | ||||||
![]() | ![]() Title: Molecular recognition of the Tes LIM2-3 domains by the actin-related protein Arp7A. Authors: Boeda, B. / Knowles, P.P. / Briggs, D.C. / Murray-Rust, J. / Soriano, E. / Garvalov, B.K. / McDonald, N.Q. / Way, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.2 KB | Display | ![]() |
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PDB format | ![]() | 49.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.2 KB | Display | ![]() |
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Full document | ![]() | 439.1 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2iybS 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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Unit cell |
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Components
#1: Protein | Mass: 7015.960 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-65 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 13343.019 Da / Num. of mol.: 1 / Fragment: EVH1 DOMAIN, RESIDUES 1-115 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Protein | Mass: 14370.611 Da / Num. of mol.: 1 / Fragment: LIM DOMAINS 2 AND 3, RESIDUES 296-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.54 % / Description: NONE |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: PROTEIN: 37.5 MG/ML OF PROTEIN COMPLEX IN 20MM TRIS-HCL PH 8.0, 100MM NACL RESERVOIR: 17.5 PEG 8K, 0.1MTRIS PH 8.5, 0.15M KSCN SITTING DROPS 2:1 PROTEIN:RESERVOIR, 22 DEG C CRYOPROTECTANT: N-PARATONE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 17, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25.74 Å / Num. obs: 12008 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 79.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IYB Resolution: 2.62→25.56 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 11.816 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.477 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.715 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→25.56 Å
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Refine LS restraints |
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