+Open data
-Basic information
Entry | Database: PDB / ID: 6w2q | ||||||
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Title | Junction 34, DHR53-DHR4 | ||||||
Components | Junction 34 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / helical bundle / designed helical repeat / computational design | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Bick, M.J. / Brunette, T.J. / Baker, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Modular repeat protein sculpting using rigid helical junctions. Authors: Brunette, T.J. / Bick, M.J. / Hansen, J.M. / Chow, C.M. / Kollman, J.M. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w2q.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w2q.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 6w2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w2q_validation.pdf.gz | 409.6 KB | Display | wwPDB validaton report |
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Full document | 6w2q_full_validation.pdf.gz | 409.6 KB | Display | |
Data in XML | 6w2q_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 6w2q_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/6w2q ftp://data.pdbj.org/pub/pdb/validation_reports/w2/6w2q | 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: 24350.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.97 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Crystals were grown in Qiagen JCSG Core III suite condition G5 (0.2M calcium chloride dihydrate, 20% (w/v) PEG 3500). Crystals were briefly soaked in crystallization condition supplemented ...Details: Crystals were grown in Qiagen JCSG Core III suite condition G5 (0.2M calcium chloride dihydrate, 20% (w/v) PEG 3500). Crystals were briefly soaked in crystallization condition supplemented with 25% (v/v) PEG 400 as a cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen vapor stream / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. obs: 18766 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Χ2: 0.791 / Net I/σ(I): 7.9 / Num. measured all: 124942 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Computational design model Resolution: 1.8→44.901 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.3 Details: Iterative rounds of manual model building in Coot and refinement in Phenix.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.73 Å2 / Biso mean: 41.0369 Å2 / Biso min: 19.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→44.901 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 31.6084 Å / Origin y: 20.8636 Å / Origin z: 51.2367 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 9 through 204) |