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Yorodumi- PDB-2vac: Structure of N-terminal Actin Depolymerizing Factor homology (ADF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vac | ||||||
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Title | Structure of N-terminal Actin Depolymerizing Factor homology (ADF-H) domain of human twinfilin-2 | ||||||
Components | TWINFILIN-2 | ||||||
Keywords | TRANSFERASE / ACTIN BINDING / PHOSPHORYLATION / COFILIN-LIKE / CYTOSKELETON / ACTIN-BINDING / PROTEIN TYROSINE KINASE-9 / ACTIN DEPOLYMERIZING FACTOR TRANSFERASE | ||||||
Function / homology | Function and homology information regulation of microvillus length / sequestering of actin monomers / negative regulation of actin filament polymerization / stereocilium / cell projection organization / barbed-end actin filament capping / actin filament depolymerization / regulation of lamellipodium assembly / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea ...regulation of microvillus length / sequestering of actin monomers / negative regulation of actin filament polymerization / stereocilium / cell projection organization / barbed-end actin filament capping / actin filament depolymerization / regulation of lamellipodium assembly / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / myofibril / actin monomer binding / positive regulation of axon extension / positive regulation of lamellipodium assembly / cellular response to retinoic acid / phosphatidylinositol-4,5-bisphosphate binding / protein kinase C binding / filopodium / actin filament / regulation of actin cytoskeleton organization / cellular response to growth factor stimulus / positive regulation of neuron projection development / actin filament binding / lamellipodium / growth cone / cadherin binding / perinuclear region of cytoplasm / RNA binding / extracellular exosome / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Elkins, J.M. / Pike, A.C.W. / King, O. / Salah, E. / Savitsky, P. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Knapp, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2 Authors: Elkins, J.M. / Pike, A.C.W. / King, O. / Salah, E. / Savitsky, P. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vac.cif.gz | 46 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vac.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 2vac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/2vac ftp://data.pdbj.org/pub/pdb/validation_reports/va/2vac | HTTPS FTP |
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-Related structure data
Related structure data | 1m4jS 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: 15181.217 Da / Num. of mol.: 1 Fragment: ACTIN DEPOLYMERIZING FACTOR HOMOLOGY (ADF-H) DOMAIN 1, RESIDUES 6-137 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: Q6IBS0 | ||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / | #4: 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: 2.01 Å3/Da / Density % sol: 38.8 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.01M ZINC CHLORIDE,10% ETHYLENE GLYCOL,20% PEG6000, 0.1M TRIS PH8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 2, 2007 / Details: MULTI-LAYER VARIMAX HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20.1 Å / Num. obs: 13653 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 18.66 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.5 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M4J Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.125 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / 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: 15.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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