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- PDB-11ot: Crystal Structure of Honey Truffle Active Component 1 through 4 w... -

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Basic information

Entry
Database: PDB / ID: 11ot
TitleCrystal Structure of Honey Truffle Active Component 1 through 4 with HEPES bound (Orthorhombic P form)
ComponentsHoney Truffle Active Component 1 through 4
KeywordsPROTEIN BINDING / Honey Truffle Active Component 1 through 4 / sweet tasting protein
Function / homologyACETATE ION
Function and homology information
Biological speciesMattirolomyces terfezioides (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsLovell, S. / Cooper, A. / Connors, D.E. / Pitkanen, T.T. / McFarland, C.T. / Vo, P. / Patnaik, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2026
Title: Crystal structures of the sweet-tasting protein honey truffle active component from Mattirolomyces terfezioides.
Authors: Pitkanen, T.T. / Cooper, A. / Vo, P. / McFarland, C.T. / Patnaik, R. / Lovell, S. / Connors, D.E.
History
DepositionMar 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Honey Truffle Active Component 1 through 4
B: Honey Truffle Active Component 1 through 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7127
Polymers26,7882
Non-polymers9245
Water8,503472
1
A: Honey Truffle Active Component 1 through 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1245
Polymers13,3941
Non-polymers7304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Honey Truffle Active Component 1 through 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5882
Polymers13,3941
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.112, 58.915, 84.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Honey Truffle Active Component 1 through 4


Mass: 13394.060 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mattirolomyces terfezioides (fungus) / Plasmid: pPpGUT1 / Production host: Komagataella phaffii (fungus) / Strain (production host): NRRLY-11430
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% (w/v) PEG 6000, 100 mM Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 23, 2025
RadiationMonochromator: HELIOS MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.25→25.31 Å / Num. obs: 66898 / % possible obs: 100 % / Redundancy: 20.5 % / CC1/2: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.019 / Rrim(I) all: 0.088 / Χ2: 1.01 / Net I/σ(I): 26.1 / Num. measured all: 1370475
Reflection shellResolution: 1.25→1.27 Å / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 1.433 / Num. measured all: 26471 / Num. unique obs: 3279 / CC1/2: 0.62 / Rpim(I) all: 0.506 / Rrim(I) all: 1.528 / Χ2: 1.14 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5750: ???)refinement
Aimlessdata scaling
SAINTdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→25.31 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1643 3327 4.98 %
Rwork0.1318 --
obs0.1334 66808 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 57 472 2409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082079
X-RAY DIFFRACTIONf_angle_d1.0392844
X-RAY DIFFRACTIONf_dihedral_angle_d15.986784
X-RAY DIFFRACTIONf_chiral_restr0.084303
X-RAY DIFFRACTIONf_plane_restr0.014359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.29061350.25752650X-RAY DIFFRACTION100
1.27-1.290.27391340.22012566X-RAY DIFFRACTION100
1.29-1.310.25191350.20132636X-RAY DIFFRACTION100
1.31-1.330.23021300.192613X-RAY DIFFRACTION100
1.33-1.350.2371300.17562610X-RAY DIFFRACTION100
1.35-1.380.17821370.16672608X-RAY DIFFRACTION100
1.38-1.40.17351470.15472606X-RAY DIFFRACTION100
1.4-1.430.21141360.14942624X-RAY DIFFRACTION100
1.43-1.460.17631340.14562628X-RAY DIFFRACTION100
1.46-1.50.18761420.14482621X-RAY DIFFRACTION100
1.5-1.530.16811460.1382592X-RAY DIFFRACTION100
1.53-1.570.1841360.12662638X-RAY DIFFRACTION100
1.57-1.620.14931390.11422637X-RAY DIFFRACTION100
1.62-1.670.18431460.11162605X-RAY DIFFRACTION100
1.67-1.730.1561590.11542637X-RAY DIFFRACTION100
1.73-1.80.12941280.11012636X-RAY DIFFRACTION100
1.8-1.880.15241560.11022618X-RAY DIFFRACTION100
1.88-1.980.1631300.11442666X-RAY DIFFRACTION100
1.98-2.110.15711540.10662664X-RAY DIFFRACTION100
2.11-2.270.14331310.11172673X-RAY DIFFRACTION100
2.27-2.50.14071270.11882662X-RAY DIFFRACTION100
2.5-2.860.13461240.1242709X-RAY DIFFRACTION100
2.86-3.60.15821400.12292730X-RAY DIFFRACTION100
3.6-25.310.14991510.14182852X-RAY DIFFRACTION100

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