+Open data
-Basic information
Entry | Database: PDB / ID: 5e5y | ||||||
---|---|---|---|---|---|---|---|
Title | Quasi-racemic snakin-1 in P1 before radiation damage | ||||||
Components |
| ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Solanum tuberosum (potato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.506 Å | ||||||
Authors | Yeung, H. / Squire, C.J. / Yosaatmadja, Y. / Panjikar, S. / Baker, E.N. / Harris, P.W.R. / Brimble, M.A. | ||||||
Funding support | New Zealand, 1items
| ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5e5y.cif.gz | 111.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5e5y.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 5e5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e5y_validation.pdf.gz | 463.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5e5y_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 5e5y_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 5e5y_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/5e5y ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e5y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 7059.083 Da / Num. of mol.: 2 / Fragment: UNP residues 26-88 / Mutation: Y25(PHI) / Source method: obtained synthetically Details: L- snakin-1 from potato containing a single substitution of p-iodophenylalanine for 25Tyr Source: (synth.) Solanum tuberosum (potato) / References: UniProt: B6E1W5, UniProt: Q948Z4*PLUS #2: Protein | Mass: 6938.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: D- enantiomer of potato snakin-1 / Source: (synth.) Solanum tuberosum (potato) / References: UniProt: Q948Z4*PLUS #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.89 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 3.8 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9199 Å |
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: 0.9199 Å / Relative weight: 1 |
Reflection | Resolution: 1.506→36.461 Å / Num. obs: 34033 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / CC1/2: 0.995 / Rpim(I) all: 0.074 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.506→1.53 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.6 / CC1/2: 0.77 / Rpim(I) all: 0.474 / % possible all: 93 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 1.506→36.461 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.52 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.506→36.461 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|