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Yorodumi- PDB-4nwo: Computationally Designed Two-Component Self-Assembling Tetrahedra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nwo | ||||||
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Title | Computationally Designed Two-Component Self-Assembling Tetrahedral Cage T33-15 | ||||||
Components |
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Keywords | PROTEIN BINDING / two-component / self-assembling / tetrahedron / designed protein cage / computational design / protein engineering / multimerization / nanomaterial / nanostructure / molybdenum cofactor biosynthesis protein / mog / chorismate mutase / isomerase | ||||||
Function / homology | Function and homology information chorismate metabolic process / chorismate mutase / chorismate mutase activity / Mo-molybdopterin cofactor biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Shewanella oneidensis (bacteria) Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | McNamara, D.E. / King, N.P. / Bale, J.B. / Sheffler, W. / Baker, D. / Yeates, T.O. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Accurate design of co-assembling multi-component protein nanomaterials. Authors: King, N.P. / Bale, J.B. / Sheffler, W. / McNamara, D.E. / Gonen, S. / Gonen, T. / Yeates, T.O. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nwo.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nwo.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nwo_validation.pdf.gz | 427.9 KB | Display | wwPDB validaton report |
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Full document | 4nwo_full_validation.pdf.gz | 429 KB | Display | |
Data in XML | 4nwo_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 4nwo_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/4nwo ftp://data.pdbj.org/pub/pdb/validation_reports/nw/4nwo | HTTPS FTP |
-Related structure data
Related structure data | 4nwnC 4nwpC 4nwqC 4nwrC 1ufyS 3k6aS 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: 19049.074 Da / Num. of mol.: 1 Mutation: Y20T, E21A, D30L, T31A, D34L, F110E, K135D, K137A, R140S, E141D, D144L, V168M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: mogA, SO_0065 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EKM7 |
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#2: Protein | Mass: 14514.650 Da / Num. of mol.: 1 Mutation: E12N, E13S, E17T, A18S, H20I, Q21I, R24I, E25L, L28E, R109S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: aroG, aroH / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q84FH6, UniProt: Q5SJY4*PLUS, chorismate mutase |
#3: Chemical | ChemComp-CA / |
#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: 3.02 Å3/Da / Density % sol: 59.29 % |
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Crystal grow | Temperature: 298 K / pH: 6.5 Details: 100 mM sodium cacodylate pH 6.5, 200 mM calcium acetate, 28% (v/v) PEG 300, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→75.491 Å / Num. obs: 10783 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.59 % / Biso Wilson estimate: 79.22 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 19.43 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 14.34 % / Rmerge(I) obs: 1.863 / Mean I/σ(I) obs: 2.25 / % possible all: 100 |
-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: 3K6A AND 1UFY Resolution: 2.8→75.49 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→75.49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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