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

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Basic information

Entry
Database: PDB / ID: 11ow
TitleCrystal Structure of Honey Truffle Active Component 1 through 4 with 1,4-butanediol bound (Orthorhombic P form)
ComponentsHoney Truffle Active Component 1 through 4
KeywordsPROTEIN BINDING / Honey Truffle Active Component 1 through 4 / sweet tasting protein / Mattirolomyces terfezioides
Function / homology1,4-BUTANEDIOL / Chem-PG6
Function and homology information
Biological speciesMattirolomyces terfezioides (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.18 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)27,2517
Polymers26,7882
Non-polymers4635
Water8,287460
1
A: Honey Truffle Active Component 1 through 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8215
Polymers13,3941
Non-polymers4274
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)13,4302
Polymers13,3941
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.201, 58.627, 84.768
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (v/v) Glycerol, 10% (w/v) PEG 4000, 0.05 M Tris, 0.05 M BICINE pH 8.5, 0.02 M 1,2-Propanediol, 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 0.01 M Spermine ...Details: 20% (v/v) Glycerol, 10% (w/v) PEG 4000, 0.05 M Tris, 0.05 M BICINE pH 8.5, 0.02 M 1,2-Propanediol, 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 0.01 M Spermine tetrahydrochloride, 0.01 M Spermidine trihydrochloride, 0.01 M 1,4-Diaminobutane dihydrochloride, 0.01 M DL-Ornithine monohydrochloride

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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: Jun 13, 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: 1.18→25.45 Å / Num. obs: 79723 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.026 / Rrim(I) all: 0.097 / Χ2: 1.01 / Net I/σ(I): 18.8 / Num. measured all: 1077965
Reflection shellResolution: 1.18→1.2 Å / % possible obs: 100 % / Redundancy: 8.7 % / Rmerge(I) obs: 1.364 / Num. measured all: 34097 / Num. unique obs: 3914 / CC1/2: 0.646 / Rpim(I) all: 0.487 / Rrim(I) all: 1.45 / Χ2: 1.15 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5740: ???)refinement
Aimlessdata scaling
SAINTdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→25.45 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.152 3984 5 %
Rwork0.1266 --
obs0.1279 79627 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.18→25.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 25 460 2365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072098
X-RAY DIFFRACTIONf_angle_d1.0152874
X-RAY DIFFRACTIONf_dihedral_angle_d13.181802
X-RAY DIFFRACTIONf_chiral_restr0.085314
X-RAY DIFFRACTIONf_plane_restr0.013363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.190.27161460.22912650X-RAY DIFFRACTION100
1.19-1.210.23521360.22312700X-RAY DIFFRACTION100
1.21-1.230.25751510.2132673X-RAY DIFFRACTION100
1.23-1.240.2191360.20992651X-RAY DIFFRACTION100
1.24-1.260.2461370.19752664X-RAY DIFFRACTION100
1.26-1.280.23191410.19162681X-RAY DIFFRACTION100
1.28-1.30.20421460.18292652X-RAY DIFFRACTION100
1.3-1.320.23211210.18072698X-RAY DIFFRACTION100
1.32-1.340.20051380.16462667X-RAY DIFFRACTION100
1.34-1.370.18541480.1562686X-RAY DIFFRACTION100
1.37-1.390.14541610.13952659X-RAY DIFFRACTION100
1.39-1.420.17451390.13082670X-RAY DIFFRACTION100
1.42-1.450.14131590.12562653X-RAY DIFFRACTION100
1.45-1.490.14591300.11822710X-RAY DIFFRACTION100
1.49-1.520.12381450.10832677X-RAY DIFFRACTION100
1.52-1.570.14481480.11092686X-RAY DIFFRACTION100
1.57-1.610.1671470.10682692X-RAY DIFFRACTION100
1.61-1.660.15951430.10592695X-RAY DIFFRACTION100
1.66-1.720.13061360.10672715X-RAY DIFFRACTION100
1.72-1.790.13321240.09842701X-RAY DIFFRACTION100
1.79-1.870.13571450.09922694X-RAY DIFFRACTION100
1.87-1.970.12141540.10332701X-RAY DIFFRACTION100
1.97-2.10.13361400.1012737X-RAY DIFFRACTION100
2.1-2.260.11591160.10192736X-RAY DIFFRACTION100
2.26-2.480.14971470.11322748X-RAY DIFFRACTION100
2.48-2.840.14711420.11932765X-RAY DIFFRACTION100
2.84-3.580.13191590.1142766X-RAY DIFFRACTION100
3.58-25.450.13391490.13512916X-RAY DIFFRACTION100

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