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- PDB-5hkr: Crystal structure of de novo designed fullerene organising protei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hkr | ||||||
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Title | Crystal structure of de novo designed fullerene organising protein complex with fullerene | ||||||
![]() | fullerene organizing protein | ||||||
![]() | DE NOVO PROTEIN / Fullerene protein complex / De novo protein design | ||||||
Function / homology | (C_{60}-I_{h})[5,6]fullerene![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Acharya, R. / Kim, Y.H. / Grigoryan, G. / DeGardo, W.F. | ||||||
![]() | ![]() Title: Protein-directed self-assembly of a fullerene crystal. Authors: Kim, K.H. / Ko, D.K. / Kim, Y.T. / Kim, N.H. / Paul, J. / Zhang, S.Q. / Murray, C.B. / Acharya, R. / DeGrado, W.F. / Kim, Y.H. / Grigoryan, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22 KB | Display | ![]() |
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PDB format | ![]() | 14.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 4.9 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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/peptide | Mass: 3188.565 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-60C / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 53.25 % Description: the entry contains Friedel pairs in F_Plus/Minus columns |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20mM sodium phosphate, 100mM NaCl pH 7.5, 17mM lithium sulfate monohydrate, 85mM tris-hcl sodium pH 8.5, 25.5% PEG 4000, 25%(v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 5598 / % possible obs: 100 % / Redundancy: 13.7 % / Rsym value: 0.135 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
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Processing
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Refinement | Resolution: 2.35→36.125 Å / Cross valid method: FREE R-VALUE / σ(F): 1.61 / Phase error: 24.16 / Stereochemistry target values: TWIN_LSQ_F Details: the entry contains Friedel pairs in F_Plus/Minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→36.125 Å
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Refine LS restraints |
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LS refinement shell |
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