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- PDB-2v90: Crystal structure of the 3rd PDZ domain of intestine- and kidney-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v90 | ||||||
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Title | Crystal structure of the 3rd PDZ domain of intestine- and kidney- enriched PDZ domain IKEPP (PDZD3) | ||||||
![]() | PDZ DOMAIN-CONTAINING PROTEIN 3 | ||||||
![]() | PROTEIN BINDING / PDZD3 / MEMBRANE / PDZ DOMAIN / PROTEIN-BINDING | ||||||
Function / homology | ![]() guanylate cyclase inhibitor activity / Intestinal infectious diseases / receptor guanylyl cyclase signaling pathway / : / water transport / apical junction complex / ion channel inhibitor activity / negative regulation of cGMP-mediated signaling / ubiquitin-specific protease binding / brush border ...guanylate cyclase inhibitor activity / Intestinal infectious diseases / receptor guanylyl cyclase signaling pathway / : / water transport / apical junction complex / ion channel inhibitor activity / negative regulation of cGMP-mediated signaling / ubiquitin-specific protease binding / brush border / monoatomic ion transport / response to toxic substance / apical part of cell / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Uppenberg, J. / Gileadi, C. / Phillips, C. / Elkins, J. / Bunkoczi, G. / Cooper, C. / Pike, A.C.W. / Salah, E. / Ugochukwu, E. / Arrowsmith, C.H. ...Uppenberg, J. / Gileadi, C. / Phillips, C. / Elkins, J. / Bunkoczi, G. / Cooper, C. / Pike, A.C.W. / Salah, E. / Ugochukwu, E. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Doyle, D.A. | ||||||
![]() | ![]() Title: Crystal Structure of the 3Rd Pdz Domain of Intestine- and Kidney-Enriched Pdz Domain Ikepp (Pdzd3) Authors: Uppenberg, J. / Gileadi, C. / Phillips, C. / Elkins, J. / Bunkoczi, G. / Cooper, C. / Pike, A.C.W. / Salah, E. / Ugochukwu, E. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Doyle, D.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.9 KB | Display | ![]() |
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PDB format | ![]() | 98.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.9 KB | Display | ![]() |
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Full document | ![]() | 477.1 KB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g9oS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
#1: Protein | Mass: 10257.568 Da / Num. of mol.: 6 / Fragment: PDZ DOMAIN, RESIDUES 246-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE LAST 4 RESIDUES (GLU336-VAL339) IS A COMMON PDZ-BINDING SEQUENCE ENGINEERED AT THE C-TERMINUS ...THE LAST 4 RESIDUES (GLU336-VAL339) IS A COMMON PDZ-BINDING SEQUENCE ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 2M (NH4)2SO4, 0.1M BIS-TRIS, PH=5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 16, 2007 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03315 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.7 Å / Num. obs: 36079 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.7 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1G9O Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.184 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.193 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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