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- PDB-11os: Crystal Structure of Honey Truffle Active Component 1 through 4 (... -

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Basic information

Entry
Database: PDB / ID: 11os
TitleCrystal Structure of Honey Truffle Active Component 1 through 4 (Orthorhombic P form)
ComponentsHoney Truffle Active Component 1 through 4
KeywordsPROTEIN BINDING / Honey Truffle Active Component 1 through 4 / sweet tasting protein / Mattirolomyces terfezioide
Biological speciesMattirolomyces terfezioides (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.23 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)27,1415
Polymers26,7882
Non-polymers3533
Water9,260514
1
A: Honey Truffle Active Component 1 through 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4653
Polymers13,3941
Non-polymers712
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)13,6762
Polymers13,3941
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.124, 59.024, 84.557
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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 45.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) PEG 4000, 100 mM Tris pH 8.0

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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 22, 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: 1.23→25.43 Å / Num. obs: 70668 / % possible obs: 100 % / Redundancy: 17.6 % / CC1/2: 1 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.02 / Rrim(I) all: 0.089 / Χ2: 1.02 / Net I/σ(I): 24 / Num. measured all: 1243052
Reflection shellResolution: 1.23→1.25 Å / % possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 1.639 / Num. measured all: 30818 / Num. unique obs: 3437 / CC1/2: 0.735 / Rpim(I) all: 0.572 / Rrim(I) all: 1.738 / Χ2: 1.15 / 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: 1.23→25.43 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1636 3608 5.13 %
Rwork0.133 --
obs0.1346 70287 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.23→25.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 19 514 2413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082039
X-RAY DIFFRACTIONf_angle_d1.0012794
X-RAY DIFFRACTIONf_dihedral_angle_d11.888758
X-RAY DIFFRACTIONf_chiral_restr0.083306
X-RAY DIFFRACTIONf_plane_restr0.015354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.250.30051220.28342447X-RAY DIFFRACTION97
1.25-1.260.29861340.27332482X-RAY DIFFRACTION97
1.26-1.280.28571280.24392467X-RAY DIFFRACTION98
1.28-1.30.24231390.22232506X-RAY DIFFRACTION99
1.3-1.320.27911560.22012501X-RAY DIFFRACTION99
1.32-1.340.25881330.20442572X-RAY DIFFRACTION100
1.34-1.370.23461370.17452521X-RAY DIFFRACTION100
1.37-1.390.18651430.1612545X-RAY DIFFRACTION100
1.39-1.420.19391450.1422551X-RAY DIFFRACTION100
1.42-1.450.18211310.13732531X-RAY DIFFRACTION100
1.45-1.480.1851270.13562590X-RAY DIFFRACTION100
1.48-1.510.15061610.13192540X-RAY DIFFRACTION100
1.51-1.550.17051580.12682541X-RAY DIFFRACTION100
1.55-1.590.13461410.11072553X-RAY DIFFRACTION100
1.59-1.640.14721300.10742556X-RAY DIFFRACTION100
1.64-1.690.16221340.10732601X-RAY DIFFRACTION100
1.69-1.750.13391420.10492546X-RAY DIFFRACTION100
1.75-1.820.13961280.10622577X-RAY DIFFRACTION100
1.82-1.90.1471410.11362608X-RAY DIFFRACTION100
1.9-2.010.13941230.11352586X-RAY DIFFRACTION100
2.01-2.130.14731480.10632576X-RAY DIFFRACTION100
2.13-2.290.1581410.11322607X-RAY DIFFRACTION100
2.3-2.530.14521450.12382603X-RAY DIFFRACTION100
2.53-2.890.15271540.12422610X-RAY DIFFRACTION100
2.89-3.640.14421300.11852682X-RAY DIFFRACTION100
3.64-25.430.14441370.13942780X-RAY DIFFRACTION100

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