+Open data
-Basic information
Entry | Database: PDB / ID: 6dlm | ||||||
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Title | DHD127 | ||||||
Components |
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Keywords | DE NOVO PROTEIN / Computational design / heterodimer / coiled-coil | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.753 Å | ||||||
Authors | Bick, M.J. / Chen, Z. / Baker, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2019 Title: Programmable design of orthogonal protein heterodimers. Authors: Chen, Z. / Boyken, S.E. / Jia, M. / Busch, F. / Flores-Solis, D. / Bick, M.J. / Lu, P. / VanAernum, Z.L. / Sahasrabuddhe, A. / Langan, R.A. / Bermeo, S. / Brunette, T.J. / Mulligan, V.K. / ...Authors: Chen, Z. / Boyken, S.E. / Jia, M. / Busch, F. / Flores-Solis, D. / Bick, M.J. / Lu, P. / VanAernum, Z.L. / Sahasrabuddhe, A. / Langan, R.A. / Bermeo, S. / Brunette, T.J. / Mulligan, V.K. / Carter, L.P. / DiMaio, F. / Sgourakis, N.G. / Wysocki, V.H. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dlm.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dlm.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 6dlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/6dlm ftp://data.pdbj.org/pub/pdb/validation_reports/dl/6dlm | HTTPS FTP |
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-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: 9119.329 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 9213.521 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#3: 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: 2.09 Å3/Da / Density % sol: 35.8 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Molecular Dimensions Morpheus condition E9 - 0.12M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1M Buffer ...Details: Molecular Dimensions Morpheus condition E9 - 0.12M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1M Buffer System 3 (1.0M Tris (base); BICINE, pH 8.5 at 20C), pH 8.5, 50% (v/v) Precipitant Mix 1 (40% v/v PEG 500* MME; 20% w/v PEG 20000) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999995 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2018 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999995 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. obs: 14674 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.048 / Rrim(I) all: 0.132 / Χ2: 1.219 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 1189 / CC1/2: 0.848 / Rpim(I) all: 0.282 / Rrim(I) all: 0.787 / Χ2: 0.599 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Computational design model Resolution: 1.753→38.817 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.77 Details: Iterative rounds of manual model building in Coot and refinement with Phenix.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.753→38.817 Å
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Refine LS restraints |
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LS refinement shell |
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