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Yorodumi- PDB-2q9v: Crystal structure of the C890S mutant of the 4th PDZ domain of hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q9v | ||||||
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Title | Crystal structure of the C890S mutant of the 4th PDZ domain of human membrane associated guanylate kinase | ||||||
Components | Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 | ||||||
Keywords | TRANSFERASE / PDZ / MEMBRANE ASSOCIATED GUANYLATE KINASE / CYS SER MUTANT / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information positive regulation of cell-cell adhesion / alpha-actinin binding / bicellular tight junction / cell projection / cell periphery / adherens junction / cell-cell junction / cell junction / protein-containing complex assembly / cell surface receptor signaling pathway ...positive regulation of cell-cell adhesion / alpha-actinin binding / bicellular tight junction / cell projection / cell periphery / adherens junction / cell-cell junction / cell junction / protein-containing complex assembly / cell surface receptor signaling pathway / cell adhesion / nucleolus / signal transduction / nucleoplasm / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pilka, E.S. / Hozjan, V. / Kavanagh, K.L. / Papagrigoriou, E. / Cooper, C. / Elkins, J.M. / Doyle, D.A. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.A. ...Pilka, E.S. / Hozjan, V. / Kavanagh, K.L. / Papagrigoriou, E. / Cooper, C. / Elkins, J.M. / Doyle, D.A. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.A. / Weigelt, J. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the C890S mutant of the 4th PDZ domain of human membrane associated guanylate kinase. Authors: Pilka, E.S. / Hozjan, V. / Kavanagh, K.L. / Papagrigoriou, E. / Cooper, C. / Elkins, J.M. / Doyle, D.A. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.A. / Weigelt, J. / Edwards, A. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q9v.cif.gz | 32.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q9v.ent.gz | 20.8 KB | Display | PDB format |
PDBx/mmJSON format | 2q9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/2q9v ftp://data.pdbj.org/pub/pdb/validation_reports/q9/2q9v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9878.229 Da / Num. of mol.: 1 / Fragment: 4th PDZ Domain / Mutation: C890S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Brain / Gene: MAGI1, BAIAP1, BAP1, TNRC19 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q96QZ7 |
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#2: Water | ChemComp-HOH / |
-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: 38.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1:2 Protein:Well solution ratio, 20% PEG 3350, 10% Ethylene glycol, 200 mM Sodium acetate, 100 mM BTP pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 5, 2007 / Details: OSMIC |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→23 Å / Num. all: 5689 / Num. obs: 5434 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.069 / Rsym value: 0.075 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.7 / Num. unique all: 759 / Rsym value: 0.313 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2I04,2PNT,2OPG Resolution: 2→20.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.67 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.187 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.589 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -0.6197 Å / Origin y: 1.2253 Å / Origin z: -1.68 Å
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