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- PDB-5e5y: Quasi-racemic snakin-1 in P1 before radiation damage -

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Basic information

Entry
Database: PDB / ID: 5e5y
TitleQuasi-racemic snakin-1 in P1 before radiation damage
Components
  • D- snakin-1
  • Snakin-1
KeywordsANTIMICROBIAL PROTEIN / GASA/snakin / cysteine-rich antimicrobial peptide
Function / homologyGibberellin regulated protein / Gibberellin regulated protein / defense response / extracellular region / FORMIC ACID / Snakin-1 / Snakin-1
Function and homology information
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.506 Å
AuthorsYeung, H. / Squire, C.J. / Yosaatmadja, Y. / Panjikar, S. / Baker, E.N. / Harris, P.W.R. / Brimble, M.A.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandUOA1115 New Zealand
CitationJournal: 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
DepositionOct 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Snakin-1
B: D- snakin-1
C: Snakin-1
D: D- snakin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,58115
Polymers27,9944
Non-polymers58611
Water4,774265
1
A: Snakin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1833
Polymers7,0591
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D- snakin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0463
Polymers6,9381
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Snakin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2134
Polymers7,0591
Non-polymers1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D- snakin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1385
Polymers6,9381
Non-polymers2004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.233, 37.415, 50.303
Angle α, β, γ (deg.)93.00, 90.58, 102.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Snakin-1


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 D- snakin-1


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 / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 3.8 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9199 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Aimless0.3.11data scaling
XDSJanuary 10, 2014data reduction
SHELXDEFORTRAN-95 VERSIONphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1667 4.9 %Free R set taken from 5E5T data
Rwork0.1792 ---
obs0.1816 34008 96.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.506→36.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 38 265 2164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062004
X-RAY DIFFRACTIONf_angle_d1.0352671
X-RAY DIFFRACTIONf_dihedral_angle_d20.9811104
X-RAY DIFFRACTIONf_chiral_restr0.072263
X-RAY DIFFRACTIONf_plane_restr0.005343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5057-1.550.29011310.23952642X-RAY DIFFRACTION94
1.55-1.60.27871350.20722632X-RAY DIFFRACTION95
1.6-1.65720.25961520.1942661X-RAY DIFFRACTION95
1.6572-1.72350.2441400.18462684X-RAY DIFFRACTION96
1.7235-1.8020.26661140.17542687X-RAY DIFFRACTION96
1.802-1.8970.22121400.17642692X-RAY DIFFRACTION97
1.897-2.01580.20921500.15022681X-RAY DIFFRACTION97
2.0158-2.17140.22361570.15712695X-RAY DIFFRACTION97
2.1714-2.38990.20371250.16652761X-RAY DIFFRACTION98
2.3899-2.73570.2311300.18212721X-RAY DIFFRACTION98
2.7357-3.44620.22121650.18762727X-RAY DIFFRACTION98
3.4462-36.47120.19941280.17772758X-RAY DIFFRACTION98

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