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Yorodumi- PDB-2wa5: Crystal structure of human filamin B actin binding domain at 1.9 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wa5 | ||||||
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Title | Crystal structure of human filamin B actin binding domain at 1.9 Angstroms resolution | ||||||
Components | FILAMIN-B | ||||||
Keywords | STRUCTURAL PROTEIN / DISEASE MUTATION / SKELETAL DYSPLASIA / ACTIN-CROSSLINKING / MYOGENESIS / CYTOSKELETON / ACTIN-BINDING / CALPONIN HOMOLOGY DOMAIN / PHOSPHOPROTEIN / DIFFERENTIATION / ATELOSTEOGENESIS / MUTANT / FILAMIN / DWARFISM / CH DOMAIN / DEVELOPMENTAL PROTEIN | ||||||
Function / homology | Function and homology information epithelial cell morphogenesis / keratinocyte development / brush border / stress fiber / skeletal muscle tissue development / phagocytic vesicle / ISG15 antiviral mechanism / Z disc / cellular response to type II interferon / actin filament binding ...epithelial cell morphogenesis / keratinocyte development / brush border / stress fiber / skeletal muscle tissue development / phagocytic vesicle / ISG15 antiviral mechanism / Z disc / cellular response to type II interferon / actin filament binding / actin cytoskeleton / actin binding / cell cortex / actin cytoskeleton organization / cadherin binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sawyer, G.M. / Clark, A.R. / Robertson, S.P. / Sutherland-Smith, A.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Disease-Associated Substitutions in the Filamin B Actin Binding Domain Confer Enhanced Actin Binding Affinity in the Absence of Major Structural Disturbance: Insights from the Crystal ...Title: Disease-Associated Substitutions in the Filamin B Actin Binding Domain Confer Enhanced Actin Binding Affinity in the Absence of Major Structural Disturbance: Insights from the Crystal Structures of Filamin B Actin Binding Domains. Authors: Sawyer, G.M. / Clark, A.R. / Robertson, S.P. / Sutherland-Smith, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wa5.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wa5.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/2wa5 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/2wa5 | HTTPS FTP |
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-Related structure data
Related structure data | 2wa6C 2wa7C 1wkuS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28135.186 Da / Num. of mol.: 1 / Fragment: ACTIN-BINDING DOMAIN, RESIDUES 2-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTB-FLNB-ABDWT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75369 | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | ChemComp-CO3 / #4: Water | ChemComp-HOH / | Sequence details | CLEAVAGE WITH RTEV PROTEASE LEAVES THE LEADER GLY ALA MET ALA STARTING AT -2. CLONING INTO NCOI ...CLEAVAGE WITH RTEV PROTEASE LEAVES THE LEADER GLY ALA MET ALA STARTING AT -2. CLONING INTO NCOI CREATED MET ALA INSTEAD OF MET AT POSITION 1. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 5.7 Details: PROTEIN WAS CRYSTALLIZED FROM 1 M LITHIUM SULFATE, 0.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PH 5.7 AND 1 MM DTT |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 29, 2006 / Details: OSMIC BLUE CONFOCAL MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20.29 Å / Num. obs: 22614 / % possible obs: 99.9 % / Observed criterion σ(I): 2.1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WKU Resolution: 1.9→20.29 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.332 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES -2-1, 132-137 ARE DISORDERED. RESIDUES GLY ALA (-2 -1) AND GLY ASP ASP ASP ALA LYS (132- 137) WERE EXCLUDED DUE TO INSUFFICIENT ELECTRON DENSITY.
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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: 22.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20.29 Å
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Refine LS restraints |
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