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Open data
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Basic information
Entry | Database: PDB / ID: 7qdj | |||||||||
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Title | Racemic structure of PK-10 and PK-11 | |||||||||
![]() | PK-10+PK-11 | |||||||||
![]() | DE NOVO PROTEIN / alpha-helical / Racemic Structure | |||||||||
Function / homology | MALONATE ION![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kumar, P. / Paterson, N.G. / Woolfson, D.N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: De novo design of discrete, stable 3 10 -helix peptide assemblies. Authors: Kumar, P. / Paterson, N.G. / Clayden, J. / Woolfson, D.N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 19.9 KB | Display | ![]() |
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PDB format | ![]() | 13.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7qdiC ![]() 7qdkC ![]() 8bfdC ![]() 8bfeC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 2036.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
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#2: Chemical | ChemComp-MLI / | ||||
#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.53 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.1M (Sodium malonate dibasic monohydrate, Imidazole, Boric acid), 25% w/v PEG1500 at pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9119 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→27.64 Å / Num. obs: 5150 / % possible obs: 97.1 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.034 / Net I/σ(I): 40.8 |
Reflection shell | Resolution: 1.44→1.47 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 19.1 / Num. unique obs: 305 / CC1/2: 1 / Rrim(I) all: 0.1 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.44→15.7 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.187 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 40.96 Å2 / Biso mean: 9.84 Å2 / Biso min: 3.95 Å2
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Refinement step | Cycle: final / Resolution: 1.44→15.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.44→1.478 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.3349 Å / Origin y: 0.9944 Å / Origin z: 2.6809 Å
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