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Open data
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Basic information
Entry | Database: PDB / ID: 3e7u | ||||||
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Title | X-ray Crystal Structure of L-Plectasin | ||||||
![]() | Plectasin![]() | ||||||
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Function / homology | ![]() potassium channel regulator activity / ![]() ![]() Similarity search - Function | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mandal, K. / Pentelute, B.L. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.H. | ||||||
![]() | ![]() Title: Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods Authors: Mandal, K. / Pentelute, B.L. / Tereshko, V. / Thammavongsa, V. / Schneewind, O. / Kossiakoff, A.A. / Kent, S.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 28.4 KB | Display | ![]() |
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PDB format | ![]() | 19.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3e7rSC 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
#1: Protein/peptide | ![]() Mass: 4415.024 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide is naturally found in Pseudoplectania nigrella (Ebony cup). References: UniProt: Q53I06 |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.32 % |
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Crystal grow![]() | Temperature: 292 K / pH: 7.5 Details: 0.1 M HEPES, 0.2 M ammonium acetate, 21% PEG 3350., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.35→50 Å / Num. obs: 15193 / % possible obs: 99.1 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 5.2 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3E7R Resolution: 1.35→23.35 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.573 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→23.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.39 Å / Total num. of bins used: 20
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