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Open data
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Basic information
Entry | Database: PDB / ID: 7l5k | ||||||
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Title | Crystal structure of the DiB-RM protein | ||||||
![]() | Lipocalin family protein | ||||||
![]() | FLUORESCENT PROTEIN / lipocalin / beta barrel / fluorogen activating protein / designed protein | ||||||
Function / homology | ISOPROPYL ALCOHOL / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bozhanova, N.G. / Harp, J.M. / Meiler, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Computational redesign of a fluorogen activating protein with Rosetta. Authors: Bozhanova, N.G. / Harp, J.M. / Bender, B.J. / Gavrikov, A.S. / Gorbachev, D.A. / Baranov, M.S. / Mercado, C.B. / Zhang, X. / Lukyanov, K.A. / Mishin, A.S. / Meiler, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.3 KB | Display | ![]() |
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PDB format | ![]() | 63.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l5lC ![]() 7l5mC ![]() 1qwdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20184.699 Da / Num. of mol.: 2 / Fragment: UNP residues 20-177 / Mutation: P22S, A36C, F53A, N76F, S89Y, E90V, L141N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-IPA / #3: Sugar | ChemComp-LMT / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.26 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 2 M ammonium sulfate, 2.5% 2-propanol, 5% w/v n-Dodecyl-b-D-maltoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 17, 2017 | ||||||||||||||||||||||||
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.86→33.32 Å / Num. obs: 36055 / % possible obs: 99.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 35.517 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.077 / Net I/σ(I): 9.1 / Num. measured all: 148895 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.354
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1QWD Resolution: 1.86→33.32 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.26 Å2 / Biso mean: 38.022 Å2 / Biso min: 24.88 Å2
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Refinement step | Cycle: final / Resolution: 1.86→33.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.908 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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