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Yorodumi- PDB-4dcl: Computationally Designed Self-assembling tetrahedron protein, T30... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dcl | ||||||
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Title | Computationally Designed Self-assembling tetrahedron protein, T308, Crystallized in space group F23 | ||||||
Components | Putative acetyltransferase SACOL2570 | ||||||
Keywords | TRANSFERASE / self assembling tetrahedron design | ||||||
Function / homology | Function and homology information galactoside O-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 Å | ||||||
Authors | Sawaya, M.R. / King, N.P. / Sheffler, W. / Baker, D. / Yeates, T.O. | ||||||
Citation | Journal: Science / Year: 2012 Title: Computational design of self-assembling protein nanomaterials with atomic level accuracy. Authors: Neil P King / William Sheffler / Michael R Sawaya / Breanna S Vollmar / John P Sumida / Ingemar André / Tamir Gonen / Todd O Yeates / David Baker / Abstract: We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify ...We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dcl.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dcl.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 4dcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dcl_validation.pdf.gz | 418.1 KB | Display | wwPDB validaton report |
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Full document | 4dcl_full_validation.pdf.gz | 418.2 KB | Display | |
Data in XML | 4dcl_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 4dcl_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/4dcl ftp://data.pdbj.org/pub/pdb/validation_reports/dc/4dcl | HTTPS FTP |
-Related structure data
Related structure data | 5438C 3vcdC 4ddfC 4eggC 3v4eS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 22990.973 Da / Num. of mol.: 1 / Mutation: Y20T, A26L, D30V, E34A, R39N, N44L, E48V, Q52A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Gene: SACOL2570 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5HCZ5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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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: 3.29 Å3/Da / Density % sol: 62.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 2.0 M sodium chloride, 0.1 M sodium acetate, pH 4.6, 35% GLYCEROL AS CRYOPROTECTANT, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.35→18.8 Å / Num. all: 4298 / Num. obs: 4298 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 81.567 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3V4E Resolution: 3.35→18.78 Å / Cor.coef. Fo:Fc: 0.9388 / Cor.coef. Fo:Fc free: 0.9093 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 221.56 Å2 / Biso mean: 135.4875 Å2 / Biso min: 38.54 Å2
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Refine analyze | Luzzati coordinate error obs: 1.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.35→18.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.35→3.75 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 13.7287 Å / Origin y: 30.6017 Å / Origin z: -11.4101 Å
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Refinement TLS group | Selection details: { A|* } |