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Yorodumi- PDB-2uzc: Structure of human PDLIM5 in complex with the C-terminal peptide ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uzc | ||||||
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Title | Structure of human PDLIM5 in complex with the C-terminal peptide of human alpha-actinin-1 | ||||||
Components | PDZ AND LIM DOMAIN 5 | ||||||
Keywords | SIGNALING PROTEIN / METAL-BINDING / ENIGMA HOMOLOG / PHOSPHORYLATION / LIM DOMAIN / PDZ DOMAIN | ||||||
Function / homology | Function and homology information muscle structure development / cell growth involved in cardiac muscle cell development / : / muscle alpha-actinin binding / cadherin binding involved in cell-cell adhesion / regulation of dendritic spine morphogenesis / actinin binding / Neurexins and neuroligins / regulation of synapse assembly / filamentous actin ...muscle structure development / cell growth involved in cardiac muscle cell development / : / muscle alpha-actinin binding / cadherin binding involved in cell-cell adhesion / regulation of dendritic spine morphogenesis / actinin binding / Neurexins and neuroligins / regulation of synapse assembly / filamentous actin / stress fiber / cell projection / adherens junction / protein kinase C binding / Z disc / actin cytoskeleton / presynapse / heart development / actin binding / actin cytoskeleton organization / postsynaptic density / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Bunkoczi, G. / Elkins, J. / Salah, E. / Burgess-Brown, N. / Papagrigoriou, E. / Pike, A.C.W. / Turnbull, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. ...Bunkoczi, G. / Elkins, J. / Salah, E. / Burgess-Brown, N. / Papagrigoriou, E. / Pike, A.C.W. / Turnbull, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / 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. / 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 | 2uzc.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uzc.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 2uzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uzc_validation.pdf.gz | 465.6 KB | Display | wwPDB validaton report |
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Full document | 2uzc_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 2uzc_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 2uzc_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uzc ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uzc | HTTPS FTP |
-Related structure data
Related structure data | 2pa1C 2pktSC 2pntC 2q3gC 2v1wC 2w7rC 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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2 |
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3 |
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4 |
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5 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 9317.584 Da / Num. of mol.: 5 / Fragment: RESIDUES 1-83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: Q8WVK0, UniProt: Q96HC4*PLUS #2: Chemical | ChemComp-CL / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE LAST 4 RESIDUES WERE TAGGED TO THE C-TERMINUS TO PROMOTE CRYSTAL CONTACTS | |
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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 Å3/Da / Density % sol: 38 % |
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Crystal grow | Details: 20% PEG3350 0.20 M KSCN |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9537 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 3, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→46.4 Å / Num. obs: 49917 / % possible obs: 79.7 % / Observed criterion σ(I): 0 / Redundancy: 2.69 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 0.83 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.98 / % possible all: 37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PKT Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.312 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.1 / 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: 16.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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