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- PDB-5oll: Crystal structure of gurmarin, a sweet taste suppressing polypeptide -

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Basic information

Entry
Database: PDB / ID: 5oll
TitleCrystal structure of gurmarin, a sweet taste suppressing polypeptide
ComponentsGurmarin
KeywordsPLANT PROTEIN / Gurmarin / sweet / taste / knottin / GPCR / inhibitor
Function / homologyGurmarin/antifungal peptide / NICKEL (II) ION / Gurmarin
Function and homology information
Biological speciesGymnema sylvestre (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsSigoillot, M. / Neiers, F. / Legrand, P. / Roblin, P. / Briand, L.
CitationJournal: Chem. Senses / Year: 2018
Title: The Crystal Structure of Gurmarin, a Sweet Taste-Suppressing Protein: Identification of the Amino Acid Residues Essential for Inhibition.
Authors: Sigoillot, M. / Brockhoff, A. / Neiers, F. / Poirier, N. / Belloir, C. / Legrand, P. / Charron, C. / Roblin, P. / Meyerhof, W. / Briand, L.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gurmarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4154
Polymers4,2391
Non-polymers1763
Water66737
1
A: Gurmarin
hetero molecules

A: Gurmarin
hetero molecules

A: Gurmarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,24512
Polymers12,7173
Non-polymers5289
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3300 Å2
ΔGint-62 kcal/mol
Surface area6520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.650, 53.650, 38.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-102-

NI

21A-103-

NI

31A-204-

HOH

41A-231-

HOH

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Components

#1: Protein/peptide Gurmarin / Sweet taste-suppressing peptide


Mass: 4238.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gymnema sylvestre (plant) / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P25810
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM MES, 5 mM MgCl2, 5 mM CaCl2, 50 mM CdCl2, 50 mM NiCl2 and 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2014 / Details: KB mirrors
RadiationMonochromator: Si crystal 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 39858 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 24.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.023 / Net I/σ(I): 18.1
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 524 / CC1/2: 0.7 / Rpim(I) all: 0.378 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→12 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.191 362 5 %RANDOM
Rwork0.19 ---
obs0.19 7238 100 %-
Displacement parametersBiso mean: 34.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.6515 Å20 Å20 Å2
2---0.6515 Å20 Å2
3---1.3029 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.45→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms293 0 3 37 333
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01341HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13469HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d122SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes11HARMONIC2
X-RAY DIFFRACTIONt_gen_planes47HARMONIC5
X-RAY DIFFRACTIONt_it341HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.86
X-RAY DIFFRACTIONt_other_torsion18.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion38SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact437SEMIHARMONIC4
LS refinement shellResolution: 1.45→1.62 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.262 103 5.01 %
Rwork0.2301 1952 -
all0.2316 2055 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 4.0763 Å / Origin y: 10.6025 Å / Origin z: 15.9414 Å
111213212223313233
T0.0261 Å2-0.014 Å2-0.0812 Å2--0.0111 Å20.0491 Å2--0.0884 Å2
L2.9403 °21.7049 °2-0.7095 °2-4.6367 °21.08 °2--2.378 °2
S-0.205 Å °-0.0156 Å °0.4939 Å °-0.3065 Å °-0.0174 Å °-0.0786 Å °-0.1273 Å °-0.0444 Å °0.2224 Å °
Refinement TLS groupSelection details: { *|* }

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