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Open data
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Basic information
Entry | Database: PDB / ID: 3e4h | ||||||
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Title | Crystal structure of the cyclotide varv F | ||||||
![]() | Varv peptide F,Varv peptide F | ||||||
![]() | PLANT PROTEIN / cyclotide / circular proteins / cystine knot / cyclization / Knottin / Plant defense | ||||||
Function / homology | Cyclotide, moebius, conserved site / Cyclotides Moebius subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / defense response / Varv peptide F![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hu, S.H. | ||||||
![]() | ![]() Title: Combined X-ray and NMR Analysis of the Stability of the Cyclotide Cystine Knot Fold That Underpins Its Insecticidal Activity and Potential Use as a Drug Scaffold Authors: Wang, C.K. / Hu, S.H. / Martin, J.L. / Hajdu, J. / Bohlin, L. / Claeson, P. / Rosengren, K.J. / Tang, J. / Tan, N.H. / Craik, D.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 | ![]() | 16.5 KB | Display | ![]() |
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PDB format | ![]() | 10.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 401.8 KB | Display | ![]() |
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Full document | ![]() | 401.8 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 4.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2k7gC ![]() 1nb1S 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 2984.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.0M MgCl2, 0.1M bicine, pH9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 6, 2000 / Details: Osmic Max-Flux optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.052 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 4978 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 35.8 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 35.6 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 8.9 / Num. unique all: 479 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1NB1 Resolution: 1.8→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.015
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