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Open data
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Basic information
Entry | Database: PDB / ID: 5e5t | ||||||
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Title | Quasi-racemic snakin-1 in P1 after radiation damage | ||||||
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![]() | ANTIMICROBIAL PROTEIN / GASA/snakin / cysteine-rich antimicrobial peptide | ||||||
Function / homology | Gibberellin regulated protein / Gibberellin regulated protein / defense response / extracellular region / FORMIC ACID / 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 | ![]() | 64.1 KB | Display | ![]() |
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PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.4 KB | Display | ![]() |
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Full document | ![]() | 458.5 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.9 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7059.083 Da / Num. of mol.: 2 / Mutation: Y25(PHI) / Source method: obtained synthetically Details: Potato L- snakin-1 containing single substitution of p-iodophenylalanine for 25Tyr Source: (synth.) ![]() ![]() #2: Protein | Mass: 6938.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: D- enantiomer of potato snakin-1 / Source: (synth.) ![]() ![]() #3: Chemical | ChemComp-FMT / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 3.8 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9919 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→36.49 Å / Num. obs: 29896 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.7 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.572→36.488 Å
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Refine LS restraints |
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LS refinement shell |
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