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- PDB-2he4: The crystal structure of the second PDZ domain of human NHERF-2 (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2he4 | ||||||
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Title | The crystal structure of the second PDZ domain of human NHERF-2 (SLC9A3R2) interacting with a mode 1 PDZ binding motif | ||||||
![]() | Na(+)/H(+) exchange regulatory cofactor NHE-RF2 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Phosphorylation / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() type 2 metabotropic glutamate receptor binding / type 3 metabotropic glutamate receptor binding / phosphatase binding / endomembrane system / protein-membrane adaptor activity / protein localization to plasma membrane / beta-catenin binding / protein-containing complex assembly / cadherin binding / apical plasma membrane ...type 2 metabotropic glutamate receptor binding / type 3 metabotropic glutamate receptor binding / phosphatase binding / endomembrane system / protein-membrane adaptor activity / protein localization to plasma membrane / beta-catenin binding / protein-containing complex assembly / cadherin binding / apical plasma membrane / focal adhesion / signaling receptor binding / extracellular exosome / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Papagrigoriou, E. / Elkins, J.M. / Berridge, G. / Gileady, O. / Colebrook, S. / Gileadi, C. / Salah, E. / Savitsky, P. / Pantic, N. / Gorrec, F. ...Papagrigoriou, E. / Elkins, J.M. / Berridge, G. / Gileady, O. / Colebrook, S. / Gileadi, C. / Salah, E. / Savitsky, P. / Pantic, N. / Gorrec, F. / Bunkoczi, G. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Doyle, D.A. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions. Authors: Elkins, J.M. / Papagrigoriou, E. / Berridge, G. / Yang, X. / Phillips, C. / Gileadi, C. / Savitsky, P. / Doyle, D.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.4 KB | Display | ![]() |
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PDB format | ![]() | 39.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.6 KB | Display | ![]() |
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Full document | ![]() | 424.6 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 9.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bygC ![]() 2fcfC ![]() 2fneC ![]() 2gzvC ![]() 2he2C ![]() 2i1nC ![]() 2iwnC ![]() 2iwoC ![]() 2iwpC ![]() 2iwqC ![]() 1g9oS ![]() 1i92S S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 9931.314 Da / Num. of mol.: 1 / Fragment: PDZ 2 Domain (Residues 147-230) / Mutation: D229G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.82 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 6, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97646 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→39.97 Å / Num. all: 13265 / Num. obs: 13060 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 0.98 % / Rmerge(I) obs: 0.0385 |
Reflection shell | Resolution: 1.45→1.55 Å / Redundancy: 0.98 % / Rmerge(I) obs: 0.1403 / Mean I/σ(I) obs: 6.45 / Num. unique all: 2349 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1i92 and 1g9o Resolution: 1.45→39.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.089 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 14.015 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→39.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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