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- PDB-5ngn: Lybatide 2, a cystine-rich peptide from Lycium barbarum -

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Basic information

Entry
Database: PDB / ID: 5ngn
TitleLybatide 2, a cystine-rich peptide from Lycium barbarum
Componentslybatide 2
KeywordsPLANT PROTEIN / cysteine-rich peptide / pi-helix / wolfberry / disulfide bonds
Function / homologyACETONITRILE / Lybatide 2
Function and homology information
Biological speciesLycium barbarum (goji berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsLei, J. / Tan, W.L. / Sakai, N. / Hilgenfeld, R.
Funding support Germany, Singapore, 4items
OrganizationGrant numberCountry
German Federal Ministry of Education and ResearchBMBF- 01DP12027 Germany
National Research Foundation in SingaporeNRF-CRP8-2011-05 Singapore
NTU iFood Research GrantM4081467.080 Singapore
NTUSGP-PROG-008 Singapore
CitationJournal: Sci Rep / Year: 2017
Title: Lybatides from Lycium barbarum Contain An Unusual Cystine-stapled Helical Peptide Scaffold.
Authors: Tan, W.L. / Wong, K.H. / Lei, J. / Sakai, N. / Tan, H.W. / Hilgenfeld, R. / Tam, J.P.
History
DepositionMar 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lybatide 2
B: lybatide 2
C: lybatide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3359
Polymers10,8843
Non-polymers4516
Water2,792155
1
A: lybatide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7613
Polymers3,6281
Non-polymers1332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: lybatide 2


Theoretical massNumber of molelcules
Total (without water)3,6281
Polymers3,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: lybatide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9455
Polymers3,6281
Non-polymers3174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)19.318, 54.655, 42.400
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide lybatide 2


Mass: 3628.035 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lycium barbarum (goji berry) / References: UniProt: A0A2D0TC93*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3N
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, pH 4.5, 2% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9184, 1.8000
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 24, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
21.81
ReflectionResolution: 1.48→41.68 Å / Num. obs: 14465 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Net I/σ(I): 44.3
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.039 / Mean I/σ(I) obs: 31.8 / Num. unique obs: 2057 / CC1/2: 0.998 / Rpim(I) all: 0.017 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.48→41.68 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.713 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.137 713 4.9 %RANDOM
Rwork0.1076 ---
obs0.10904 13735 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.561 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.11 Å2
2--0.06 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.48→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms728 0 31 155 914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02778
X-RAY DIFFRACTIONr_bond_other_d0.0020.02637
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9821052
X-RAY DIFFRACTIONr_angle_other_deg1.23731497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.585597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9626.36433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.03515117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.125153
X-RAY DIFFRACTIONr_chiral_restr0.1450.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021875
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02156
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.880.683391
X-RAY DIFFRACTIONr_mcbond_other0.8540.68390
X-RAY DIFFRACTIONr_mcangle_it1.3681.016484
X-RAY DIFFRACTIONr_mcangle_other1.3711.018485
X-RAY DIFFRACTIONr_scbond_it1.8230.989387
X-RAY DIFFRACTIONr_scbond_other1.8210.995388
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5881.341568
X-RAY DIFFRACTIONr_long_range_B_refined7.29713.7471025
X-RAY DIFFRACTIONr_long_range_B_other7.29313.7791026
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.479→1.517 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.158 58 -
Rwork0.094 962 -
obs--97.05 %

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