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Yorodumi- PDB-2v1w: Crystal structure of human LIM protein RIL (PDLIM4) PDZ domain bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v1w | ||||||
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Title | Crystal structure of human LIM protein RIL (PDLIM4) PDZ domain bound to the C-terminal peptide of human alpha-actinin-1 | ||||||
Components | PDZ AND LIM DOMAIN PROTEIN 4 | ||||||
Keywords | STRUCTURAL PROTEIN / ACTIN / STRESS / FIBRE DYNAMICS / CYTOSKELETON / LIM DOMAIN / METAL-BINDING / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information recycling endosome lumen / muscle structure development / excitatory chemical synaptic transmission / muscle alpha-actinin binding / alpha-actinin binding / filamentous actin / stress fiber / early endosome lumen / adherens junction / Z disc ...recycling endosome lumen / muscle structure development / excitatory chemical synaptic transmission / muscle alpha-actinin binding / alpha-actinin binding / filamentous actin / stress fiber / early endosome lumen / adherens junction / Z disc / recycling endosome membrane / lamellipodium / actin binding / heart development / actin cytoskeleton organization / postsynaptic membrane / early endosome membrane / protein phosphatase binding / dendritic spine / cytoskeleton / perinuclear region of cytoplasm / protein homodimerization activity / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Soundararajan, M. / Shrestha, L. / Pike, A.C.W. / Salah, E. / Burgess-Brown, N. / Elkins, J. / Umeano, C. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. ...Soundararajan, M. / Shrestha, L. / Pike, A.C.W. / Salah, E. / Burgess-Brown, N. / Elkins, J. / Umeano, C. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Doyle, D. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: Unusual Binding Interactions in Pdz Domain Crystal Structures Help Explain Binding Mechanisms. Authors: Elkins, J.M. / Gileadi, C. / Shrestha, L. / Phillips, C. / Wang, J. / Muniz, J.R.C. / 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 | 2v1w.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v1w.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/2v1w ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v1w | HTTPS FTP |
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-Related structure data
Related structure data | 2pa1C 2pktC 2pntC 2q3gC 2uzcC 2w7rC 1gq4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.06158, -0.90199, 0.42735), Vector: Details | ENTITY CRYSTALLISED CONTAINS AN ARTIFICIAL OLIGOMERISATIONC-TERMINAL TAG THAT ALLOWS MODULES TO SELF-ASSOCIATE | |
-Components
#1: Protein | Mass: 9584.851 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN, RESIDUES 1-85 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-PRARE2 / References: UniProt: P50479 #2: Chemical | ChemComp-EDO / | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-1PE / | #5: 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: 2.68 Å3/Da / Density % sol: 54.05 % |
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Crystal grow | pH: 8.5 Details: 20% PEG 10000, 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH8.5, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00234 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00234 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→61.55 Å / Num. obs: 16891 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 21.07 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GQ4 Resolution: 1.9→61.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.714 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.124 / 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: 19.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→61.55 Å
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Refine LS restraints |
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