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

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Basic information

Entry
Database: PDB / ID: 11ox
TitleCrystal Structure of Honey Truffle Active Component 1 through 4 with glucose bound (Monoclinic P form)
ComponentsHoney Truffle Active Component 1 through 4
KeywordsPROTEIN BINDING / Honey Truffle Active Component 1 through 4 / sweet tasting protein
Function / homologybeta-D-glucopyranose
Function and homology information
Biological speciesMattirolomyces terfezioides (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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)27,0044
Polymers26,7882
Non-polymers2162
Water3,567198
1
A: Honey Truffle Active Component 1 through 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6103
Polymers13,3941
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Honey Truffle Active Component 1 through 4


Theoretical massNumber of molelcules
Total (without water)13,3941
Polymers13,3941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.638, 44.472, 63.748
Angle α, β, γ (deg.)90.00, 106.68, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12.5% (v/v) MPD, 12.5% PEG 1000, 12.5% (w/v) PEG 3350, 0.05M Sodium HEPES, 0.05M MOPS pH 7.5, 0.02 M D-Glucose, 0.02 M D-Mannose, 0.02 M D-Galactose, 0.02 M L-Fucose, 0.02 M D-Xylose, 0.02 M ...Details: 12.5% (v/v) MPD, 12.5% PEG 1000, 12.5% (w/v) PEG 3350, 0.05M Sodium HEPES, 0.05M MOPS pH 7.5, 0.02 M D-Glucose, 0.02 M D-Mannose, 0.02 M D-Galactose, 0.02 M L-Fucose, 0.02 M D-Xylose, 0.02 M N-Acetyl-D-Glucosamine, 0.5 mM Manganese(II) chloride tetrahydrate, 0.5 mM Cobalt chloride hexahydrate, 0.5 mM Nickel chloride hexahydrate, 0.5 mM Zinc acetate dihydrate

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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 12, 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: 1.7→25.17 Å / Num. obs: 26884 / % possible obs: 99.1 % / Redundancy: 13.8 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.014 / Rrim(I) all: 0.055 / Χ2: 1.03 / Net I/σ(I): 28.3 / Num. measured all: 370664
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 96.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 1.566 / Num. measured all: 10431 / Num. unique obs: 1378 / CC1/2: 0.767 / Rpim(I) all: 0.602 / Rrim(I) all: 1.68 / Χ2: 1.2 / 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: 1.7→20.89 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 1299 4.87 %
Rwork0.1888 --
obs0.1911 26690 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→20.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 13 198 2084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091936
X-RAY DIFFRACTIONf_angle_d1.0192638
X-RAY DIFFRACTIONf_dihedral_angle_d17.109696
X-RAY DIFFRACTIONf_chiral_restr0.065292
X-RAY DIFFRACTIONf_plane_restr0.012335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.36741580.33122752X-RAY DIFFRACTION97
1.77-1.850.38691370.2792766X-RAY DIFFRACTION97
1.85-1.950.31881330.26272790X-RAY DIFFRACTION98
1.95-2.070.29831480.2292790X-RAY DIFFRACTION98
2.07-2.230.27411650.22672791X-RAY DIFFRACTION98
2.23-2.450.2561530.20792808X-RAY DIFFRACTION98
2.45-2.80.26471460.19992832X-RAY DIFFRACTION99
2.81-3.530.22981320.17092900X-RAY DIFFRACTION99
3.53-20.890.16261270.14182962X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.09550.771-0.29751.55861.0561.3667-0.08350.11290.0095-0.179-0.0936-0.57960.02350.8619-0.06920.22060.05630.08850.37660.05320.306410.463-6.1581.565
23.4763-2.58761.54714.8164-0.01243.1139-0.15240.0310.38470.2815-0.1182-1.0036-0.12191.56610.30710.23250.05330.05770.59580.07270.389214.274-5.397.591
32.78320.94670.21293.22912.37881.866-0.016-0.2238-0.03850.26880.0074-1.50970.25351.5689-0.06250.25760.0910.03960.82680.0790.638619.958-9.1525.091
42.42670.2948-0.02962.3994-0.31662.7620.010.2263-0.2258-0.1834-0.0275-0.16020.20390.7581-0.08070.22440.07270.06220.333-0.00870.23017.845-12.3723.711
57.8696-2.0138-0.17546.0069-1.8546.08790.14580.35220.0688-0.67470.06240.0580.05940.2452-0.18540.3051-0.0380.00420.1729-0.04370.21130.879-10.194-4.564
62.6905-0.13250.25121.9743-0.41761.1236-0.1523-1.2814-0.74070.19320.7036-0.62860.41780.77150.65060.49330.38510.39610.92970.11640.510619.58-15.183-6.224
76.4645-4.16612.16.6346-2.14765.3267-0.03810.619-0.2877-0.4769-0.1992-0.322-0.13590.85640.15760.4188-0.01250.11950.3220.03460.27527.845-6.757-7.551
84.9633-1.6074-1.92613.34350.88615.28170.1731-0.4820.00910.2691-0.21650.01010.08070.25370.0360.3038-0.0709-0.02470.2263-0.01110.1396-1.254-6.86827.535
91.7865-2.1059-0.00995.818-2.89222.4941-0.3094-0.4315-0.49170.39020.0647-0.86991.72421.28750.29040.86720.3709-0.09320.59840.21990.19458.848-18.19131.779
104.8548-1.86661.22425.2587-0.23841.5122-0.0158-0.74730.07110.95910.2118-0.0046-0.35780.2049-0.13230.4449-0.0848-0.01960.4649-0.08480.1663-0.614-3.07233.348
116.9253-1.61141.24483.7944-1.87482.59050.1515-0.33230.15280.6468-0.2331-0.87720.55041.00160.11190.48340.1085-0.13720.53560.0130.28339.392-10.54428.491
122.7811-0.4726-1.28312.64061.72466.0149-0.0253-0.0784-0.24720.2813-0.22490.18980.4252-0.26860.16670.236-0.03740.00110.1586-0.00520.1805-3.371-9.68821.757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:25 )A2 - 25
2X-RAY DIFFRACTION2( CHAIN A AND RESID 26:43 )A26 - 43
3X-RAY DIFFRACTION3( CHAIN A AND RESID 44:57 )A44 - 57
4X-RAY DIFFRACTION4( CHAIN A AND RESID 58:86 )A58 - 86
5X-RAY DIFFRACTION5( CHAIN A AND RESID 87:104 )A87 - 104
6X-RAY DIFFRACTION6( CHAIN A AND RESID 105:111 )A105 - 111
7X-RAY DIFFRACTION7( CHAIN A AND RESID 112:120 )A112 - 120
8X-RAY DIFFRACTION8( CHAIN B AND RESID 3:25 )B3 - 25
9X-RAY DIFFRACTION9( CHAIN B AND RESID 26:32 )B26 - 32
10X-RAY DIFFRACTION10( CHAIN B AND RESID 33:43 )B33 - 43
11X-RAY DIFFRACTION11( CHAIN B AND RESID 44:57 )B44 - 57
12X-RAY DIFFRACTION12( CHAIN B AND RESID 58:120 )B58 - 120

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