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- PDB-5e5t: Quasi-racemic snakin-1 in P1 after radiation damage -

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Basic information

Entry
Database: PDB / ID: 5e5t
TitleQuasi-racemic snakin-1 in P1 after 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: 1.572 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
Revision 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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)28,36511
Polymers27,9944
Non-polymers3707
Water4,450247
1
A: Snakin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2294
Polymers7,0591
Non-polymers1703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D- snakin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9842
Polymers6,9381
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Snakin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1052
Polymers7,0591
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 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
MethodPISA
Unit cell
Length a, b, c (Å)31.256, 37.442, 50.391
Angle α, β, γ (deg.)92.96, 90.55, 102.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Snakin-1 / Uncharacterized 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.) 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 40.08 %
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: 0.9919 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: 0.9919 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Aimless0.3.11data scaling
XDSJanuary 10, 2014data reduction
SHELXDEFORTRAN-95 VERSIONphasing
RefinementMethod to determine structure: MIR / Resolution: 1.572→36.488 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 1479 4.95 %Random selection
Rwork0.2046 ---
obs0.2065 29872 96.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.572→36.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 24 247 2134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062004
X-RAY DIFFRACTIONf_angle_d1.0542681
X-RAY DIFFRACTIONf_dihedral_angle_d19.4991103
X-RAY DIFFRACTIONf_chiral_restr0.072263
X-RAY DIFFRACTIONf_plane_restr0.005347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5716-1.62230.28761430.23662492X-RAY DIFFRACTION94
1.6223-1.68030.29791400.23242530X-RAY DIFFRACTION95
1.6803-1.74760.22321240.20712579X-RAY DIFFRACTION95
1.7476-1.82710.27731140.20822574X-RAY DIFFRACTION96
1.8271-1.92340.2511460.21372560X-RAY DIFFRACTION96
1.9234-2.04390.22681490.18922573X-RAY DIFFRACTION97
2.0439-2.20170.20881390.19572616X-RAY DIFFRACTION97
2.2017-2.42320.23021180.2032611X-RAY DIFFRACTION97
2.4232-2.77380.29341260.21552620X-RAY DIFFRACTION98
2.7738-3.49420.24021570.2112613X-RAY DIFFRACTION98
3.4942-36.49820.22091230.18752625X-RAY DIFFRACTION97

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