+Open data
-Basic information
Entry | Database: PDB / ID: 6abr | ||||||
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Title | Actin interacting protein 5 (Aip5, wild type) | ||||||
Components | Actin binding protein | ||||||
Keywords | STRUCTURAL PROTEIN | ||||||
Function / homology | cellular bud / Glutaredoxin domain profile. / Thioredoxin-like superfamily / cytoplasm / Uncharacterized protein YFR016C Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.002 Å | ||||||
Authors | Sun, J. / Xie, Y. / Toh, J.D.W. / Hong, W. / MIao, Y. / Gao, Y.G. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Polarisome scaffolder Spa2-mediated macromolecular condensation of Aip5 for actin polymerization. Authors: Xie, Y. / Sun, J. / Han, X. / Tursic-Wunder, A. / Toh, J.D.W. / Hong, W. / Gao, Y.G. / Miao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6abr.cif.gz | 51.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6abr.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 6abr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6abr_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 6abr_full_validation.pdf.gz | 437.6 KB | Display | |
Data in XML | 6abr_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 6abr_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/6abr ftp://data.pdbj.org/pub/pdb/validation_reports/ab/6abr | HTTPS FTP |
-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: 14282.879 Da / Num. of mol.: 2 / Fragment: UNP residues 1110-1233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: YFR016C / Production host: Escherichia coli (E. coli) / References: UniProt: P43597 #2: 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: 1.54 Å3/Da / Density % sol: 20.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCL pH 7.0, 20% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.000,0.9788,0.9636 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 29, 2016 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. obs: 11332 / % possible obs: 96.8 % / Redundancy: 3.8 % / Rsym value: 0.052 / Net I/σ(I): 19.4 | ||||||||||||
Reflection shell | Resolution: 2→2.1 Å / Num. unique obs: 943 / Rsym value: 0.142 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.002→32.715 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.002→32.715 Å
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Refine LS restraints |
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LS refinement shell |
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