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Open data
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Basic information
Entry | Database: PDB / ID: 5e5q | ||||||
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Title | Racemic snakin-1 in P21/c | ||||||
![]() | Snakin-1 | ||||||
![]() | ANTIMICROBIAL PROTEIN / GASA/snakin / cysteine-rich antimicrobial peptide | ||||||
Function / homology | Gibberellin regulated protein / Gibberellin regulated protein / defense response / extracellular region / Snakin-1 / Snakin-1![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yeung, H. / Squire, C.J. / Yosaatmadja, Y. / Panjikar, S. / Baker, E.N. / Harris, P.W.R. / Brimble, M.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily. Authors: Yeung, H. / Squire, C.J. / Yosaatmadja, Y. / Panjikar, S. / Lopez, G. / Molina, A. / Baker, E.N. / Harris, P.W. / Brimble, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64 KB | Display | ![]() |
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PDB format | ![]() | 51.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.7 KB | Display | ![]() |
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Full document | ![]() | 419.2 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11.4 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 6949.185 Da / Num. of mol.: 2 / Fragment: UNP residues 26-88 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M dibasic sodium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→34.142 Å / Num. obs: 33736 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / CC1/2: 0.997 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.5 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: In house Resolution: 1.6→34.142 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.37 / Stereochemistry target values: ML
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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: 1.6→34.142 Å
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Refine LS restraints |
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LS refinement shell |
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