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Yorodumi- PDB-4x3n: Crystal structure of 34 kDa F-actin bundling protein from Dictyos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x3n | ||||||
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Title | Crystal structure of 34 kDa F-actin bundling protein from Dictyostelium discoideum | ||||||
Components | Calcium-regulated actin-bundling protein | ||||||
Keywords | PROTEIN BINDING / actin / cytoskeleton / bundling | ||||||
Function / homology | Function and homology information intranuclear rod / parallel actin filament bundle assembly / actin crosslink formation / cortical cytoskeleton / pseudopodium / actin filament bundle assembly / phagocytic vesicle / filopodium / actin filament binding / calcium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 Å | ||||||
Authors | Kim, M.-K. / Kim, J.-H. / Kim, J.-S. / Kang, S.-O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structure of the 34 kDa F-actin-bundling protein ABP34 from Dictyostelium discoideum. Authors: Kim, M.K. / Kim, J.H. / Kim, J.S. / Kang, S.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x3n.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x3n.ent.gz | 138.9 KB | Display | PDB format |
PDBx/mmJSON format | 4x3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/4x3n ftp://data.pdbj.org/pub/pdb/validation_reports/x3/4x3n | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 33396.840 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: abpB, DDB_G0279081 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P24005 #2: Chemical | #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: ammonium acetate, sodium citrate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 12, 2010 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→72.19 Å / Num. obs: 72226 / % possible obs: 98.9 % / Redundancy: 9.6 % / Rsym value: 0.078 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 5.4 % / % possible all: 88.2 |
-Processing
Software |
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Refinement | Resolution: 1.89→72.19 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.686 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.152 / 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: 35.158 Å2
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Refinement step | Cycle: 1 / Resolution: 1.89→72.19 Å
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