+Open data
-Basic information
Entry | Database: PDB / ID: 2iwo | ||||||
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Title | 12th PDZ domain of Multiple PDZ Domain Protein MPDZ | ||||||
Components | MULTIPLE PDZ DOMAIN PROTEIN | ||||||
Keywords | SIGNALING PROTEIN / SGC / MUPP1 / MUPP-1 / PDZ DOMAIN / HOST-VIRUS INTERACTION / STRUCTURAL GENOMICS CONSORTIUM / SYNAPTOSOME / TIGHT JUNCTION / ALTERNATIVE SPLICING | ||||||
Function / homology | Function and homology information tight junction assembly / microtubule organizing center organization / apicolateral plasma membrane / bicellular tight junction / regulation of microtubule cytoskeleton organization / apical part of cell / postsynaptic density / apical plasma membrane / dendrite / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Elkins, J.M. / Yang, X. / Gileadi, C. / Schoch, G. / Johansson, C. / Savitsky, P. / Berridge, G. / Smee, C.E.A. / Turnbull, A. / Pike, A. ...Elkins, J.M. / Yang, X. / Gileadi, C. / Schoch, G. / Johansson, C. / Savitsky, P. / Berridge, G. / Smee, C.E.A. / Turnbull, A. / Pike, A. / Papagrigoriou, E. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Doyle, D.A. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iwo.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iwo.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 2iwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/2iwo ftp://data.pdbj.org/pub/pdb/validation_reports/iw/2iwo | HTTPS FTP |
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-Related structure data
Related structure data | 2bygC 2fcfC 2fneSC 2gzvC 2he2C 2he4C 2i1nC 2iwnC 2iwpC 2iwqC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.72219, -0.10791, -0.68323), Vector: Details | BIOLOGICAL ASSEMBLY: MONOMERIC IN SOLUTION | |
-Components
#1: Protein | Mass: 12550.251 Da / Num. of mol.: 2 / Fragment: 12TH PDZ DOMAIN, RESIDUES 1831-1923 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 ROSETTA / References: UniProt: O75970 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.6 % |
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Crystal grow | pH: 7.5 / Details: 2M (NH4)2SO4, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8983 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8983 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.21 Å / Num. obs: 21145 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FNE Resolution: 1.7→53.3 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.929 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→53.3 Å
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Refine LS restraints |
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