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- PDB-5w2d: Crystal structure of mutant CJ YCEI protein (CJ-G34C) for nanotec... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w2d | ||||||
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Title | Crystal structure of mutant CJ YCEI protein (CJ-G34C) for nanotechnology applications | ||||||
![]() | Polyisoprenoid-binding protein | ||||||
![]() | UNKNOWN FUNCTION / nanomaterial nanoporous | ||||||
Function / homology | ![]() Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Lipocalin / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, T.R. / Snow, C.D. | ||||||
![]() | ![]() Title: Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals. Authors: Huber, T.R. / McPherson, E.C. / Keating, C.E. / Snow, C.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.7 KB | Display | ![]() |
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PDB format | ![]() | 33.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.5 KB | Display | ![]() |
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Full document | ![]() | 438.7 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w17SC ![]() 5w2kC ![]() 5w2rC ![]() 5w2vC ![]() 5w2xC ![]() 5w2zC ![]() 5w30C ![]() 5w31C ![]() 5w32C ![]() 5w37C ![]() 5w39C ![]() 5w3aC ![]() 5w3bC ![]() 5w3cC 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20245.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-UNL / Mass: 282.547 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.79 Å3/Da / Density % sol: 78.74 % / Mosaicity: 0.15 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3.2 M Ammonium Sulfate, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Dec 2, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→38.73 Å / Num. all: 13638 / Num. obs: 13638 / % possible obs: 99.9 % / Redundancy: 20.6 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.214 / Rsym value: 0.208 / Net I/av σ(I): 3.4 / Net I/σ(I): 13.2 / Num. measured all: 280434 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5W17 Resolution: 2.7→38.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 14.739 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.243 / Details: 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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 189.11 Å2 / Biso mean: 92.219 Å2 / Biso min: 50.51 Å2
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Refinement step | Cycle: final / Resolution: 2.7→38.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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