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Yorodumi- PDB-2pkt: Crystal structure of the human CLP-36 (PDLIM1) bound to the C-ter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pkt | ||||||
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Title | Crystal structure of the human CLP-36 (PDLIM1) bound to the C-terminal peptide of human alpha-actinin-1 | ||||||
Components | PDZ and LIM domain protein 1 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PDZ DOMAIN / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information establishment or maintenance of actin cytoskeleton polarity / muscle structure development / muscle alpha-actinin binding / maintenance of cell polarity / cadherin binding involved in cell-cell adhesion / fibroblast migration / stress fiber assembly / filamentous actin / stress fiber / adherens junction ...establishment or maintenance of actin cytoskeleton polarity / muscle structure development / muscle alpha-actinin binding / maintenance of cell polarity / cadherin binding involved in cell-cell adhesion / fibroblast migration / stress fiber assembly / filamentous actin / stress fiber / adherens junction / Z disc / heart development / actin binding / actin cytoskeleton organization / response to oxidative stress / transcription regulator complex / transcription coactivator activity / cytoskeleton / response to hypoxia / focal adhesion / regulation of transcription by RNA polymerase II / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Uppenberg, J. / Gileadi, C. / Elkins, J. / Bray, J. / Burgess-Brown, N. / Salah, E. / Gileadi, O. / Bunkoczi, G. / Ugochukwu, E. / Umeano, C. ...Uppenberg, J. / Gileadi, C. / Elkins, J. / Bray, J. / Burgess-Brown, N. / Salah, E. / Gileadi, O. / Bunkoczi, G. / Ugochukwu, E. / Umeano, C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC) | ||||||
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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Remark 999 | SEQUENCE C-TERMINAL RESIDUES 87-90 (GLU-SER-ASP-LEU) CORRESPOND TO THE C-TERMINAL TAIL OF HUMAN ... SEQUENCE C-TERMINAL RESIDUES 87-90 (GLU-SER-ASP-LEU) CORRESPOND TO THE C-TERMINAL TAIL OF HUMAN ALPHA-ACTININ-1, UNIPROT ENTRY ACTN1_HUMAN, ACCESSION CODE P12814, SEQUENCE POSITION 889-892. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pkt.cif.gz | 36.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pkt.ent.gz | 23.3 KB | Display | PDB format |
PDBx/mmJSON format | 2pkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pkt_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 2pkt_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 2pkt_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 2pkt_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/2pkt ftp://data.pdbj.org/pub/pdb/validation_reports/pk/2pkt | HTTPS FTP |
-Related structure data
Related structure data | 2pa1C 2pntC 2q3gC 2uzcC 2v1wC 2w7rC 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 9732.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Heart / Gene: PDLIM1, CLIM1, CLP36 / Plasmid: PNIC28-BSA4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00151 |
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-Non-polymers , 6 types, 111 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-PEG / | #7: 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: 2.74 Å3/Da / Density % sol: 55.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 40% PEG 300, 0.2M Calcium acetate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.79987 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2007 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.79987 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 18632 / Num. obs: 18632 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2617 / % possible all: 89.6 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in-house model Resolution: 1.5→41.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.157 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.077 / ESU R Free: 0.076 / 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: 7.375 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→41.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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