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- PDB-8zxt: sweet protein MNEI-Mut 6-3 -

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Basic information

Entry
Database: PDB / ID: 8zxt
Titlesweet protein MNEI-Mut 6-3
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / a kind of food protein
Function / homologyMonellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / Cystatin superfamily / Monellin chain A / Monellin chain B
Function and homology information
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYou, T.J. / Liu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Structural Basis for the Exceptional Thermal Stability of the Boiling-Resistant Sweet Protein MNEI
Authors: You, T. / Shi, S. / Chen, C. / Li, J. / Xu, J. / Ma, M. / Zhu, P. / Qi, T. / Dong, T. / Wang, Y. / Ye, S. / Liu, S.
History
DepositionJun 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monellin chain B,Monellin chain A
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)22,6262
Polymers22,6262
Non-polymers00
Water4,630257
1
A: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,3131
Polymers11,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,3131
Polymers11,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.627, 60.993, 65.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Monellin chain B,Monellin chain A / Monellin chain II / Monellin chain I


Mass: 11312.838 Da / Num. of mol.: 2 / Mutation: I5E,E23A,I26R,Y65I,G83E,N90D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02882, UniProt: P02881
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / Details: PEG 6000 30% BIS-TRIS Propone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.94138 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94138 Å / Relative weight: 1
ReflectionResolution: 1.43→27.28 Å / Num. obs: 16096 / % possible obs: 99.8 % / Redundancy: 9 % / Biso Wilson estimate: 12.56 Å2 / CC1/2: 0.98 / Net I/σ(I): 51.9
Reflection shellResolution: 1.43→1.45 Å / Num. unique obs: 37657 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.19_4092model building
PHENIX1.19_4092refinement
HKL-3000data reduction
PHENIX1.19_4092phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IV7

1iv7


Resolution: 1.9→27.28 Å / SU ML: 0.2261 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.9964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2682 831 5.16 %
Rwork0.2229 15265 -
obs0.2253 16096 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 0 257 1853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341634
X-RAY DIFFRACTIONf_angle_d0.61492196
X-RAY DIFFRACTIONf_chiral_restr0.0451218
X-RAY DIFFRACTIONf_plane_restr0.0063290
X-RAY DIFFRACTIONf_dihedral_angle_d5.6876218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.28721280.22722488X-RAY DIFFRACTION99.7
2.02-2.180.29211310.22372531X-RAY DIFFRACTION99.92
2.18-2.40.30471350.22712499X-RAY DIFFRACTION100
2.4-2.740.25561290.24182547X-RAY DIFFRACTION99.89
2.74-3.450.26071510.21892557X-RAY DIFFRACTION100
3.45-27.280.25241570.21282643X-RAY DIFFRACTION99.04
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)
14.595079759521.708279142092.003320847982.63791002627-0.1297947846473.19026754245-0.0676860156651-0.2783574336410.323365258715-0.144438193288-0.08744392812130.479192833939-0.0997974431642-0.7153035953710.1338714612480.1519045531890.00168344971912-0.01458123115750.226058258327-0.1007054202430.30202672234518.768649019561.475603739851.1759353888
22.02661894666-1.05292165725-2.174847734543.368421211771.767736229624.67427532146-0.207017935278-0.255576935027-0.1323438914170.208627738992-0.1010702721130.1238430252850.3314396813790.1027820373970.1935061743580.1053151333760.005085669783740.01626826964320.118303471647-0.0243513450810.08865385333532.821519438349.246265155752.9601656389
30.195800378296-0.0847289631354-0.09217124612740.4186427992470.03296867216210.355321725527-0.1035405540480.0518248559588-0.0458699165490.0921908974186-0.1090142315260.144215747480.0777713010352-0.1559975617-0.5499937439410.139032565566-0.00752851219989-0.008528495124060.132208089771-0.218811183980.20974911645323.41972299558.238657649350.9609276647
43.13921960946-1.04121697665-2.221160571861.20490461021.221786688552.70067686216-0.07713455215090.339204613312-0.302666420029-0.0207052438634-0.1486943238350.2255656828720.173292863965-0.2787266702830.1979507190940.311033717368-0.07196792468280.1645839025850.500414340979-0.3045223220840.5303591418031.96523793549.674889949956.5922746549
52.5718224829-0.0184040402823-1.242780435870.705508826619-0.0123907914071.39020562988-0.0857639831244-0.07251245897380.124626210220.095870749653-0.1021781470240.2752509682140.10527473165-0.1869229763630.09543171971350.0987787252328-0.0137874055659-0.0003531073965340.176848639025-0.09480610210550.17064270059625.36578936653.299771052249.8560477013
62.55179951462-0.055247712286-1.377802091671.35542380184-0.1601219883632.41040573368-0.0497268387662-0.125846404376-0.1154701337750.152218025658-0.2078061208630.288248445043-0.0342433916542-0.1776887005630.1022236619920.119455313324-0.01879353980620.02432657694480.223791616389-0.06487519242180.15364134723424.071437750350.282966893751.1053221625
72.20592609921-2.422309648381.990161362856.9314542535-2.869781923897.71129371433-0.07960691700410.3094609046010.3924133920390.0638450938158-0.0822244772127-0.469263709656-0.004536182402820.7595491540230.2000436650940.139628627046-0.07258954500330.01890163466810.1536304690390.03478266949430.18321468029130.549494519862.829186813429.7394375297
84.158756438082.43190897484-0.7131951943628.2774790004-0.3206238232881.92705712274-0.1119598813350.2764230659950.0548146769168-0.341533890469-0.197368201066-0.196961333144-0.0786423071150.1228364611270.2696695219650.0838931833794-0.0159835439636-0.02225673943090.1482290620.009351435172910.079571536847118.663763507752.463353193824.240188083
91.890360357160.2760547395030.1740063273714.873201969810.6670887801070.6744939898250.186929973929-0.153542927981-0.06103055911250.184425416052-0.0914708196770.1040604657290.287864900859-0.05414993489070.04132156740570.184482911557-0.103255940303-0.02711753447880.19477923339-0.005544028405920.10805726048411.077970024646.950476157831.0364300811
100.4439052103430.0264604448780.09152782928380.262483493014-0.1415176808750.16870452381-0.06474450848-0.003011601322090.07894807153620.0445124668056-0.00840848264092-0.0363965130278-0.10363930043-0.000783548351323-0.1224312489340.124512419544-0.000768805800587-0.06776961743020.05408522230120.09310547600930.18813531712826.034020719359.854117507729.3290773749
110.6632767174260.0123403571179-0.4993480570180.8515184332980.3760450318440.870285866296-0.0557031624482-0.146846033505-0.1424637438950.1896131400250.1096193018080.08459529314840.104212107958-0.0641617464564-0.1150509750040.1933109540220.05394065688180.01133017176220.3460144735960.2893119201550.42483347064547.876179817451.681721858924.3082210197
124.198869168040.324808404073-1.487160926430.640733919182-0.4576957406421.53263494707-0.0342067785089-0.01687620405020.07086542355650.0106690275734-0.0488877243516-0.07599101848050.2181060814310.157673738110.1342819409760.0624499199742-0.0278739056761-0.05510859808010.1576410888050.02908378469660.077391794238627.392728366355.616301407228.6115243928
133.88317124575-1.14495929627-0.6028666662790.982320361450.6781899691571.74301757083-0.1090238682270.07550378886190.0816773706812-0.01729953157530.01151496043430.0562736565408-0.00396388507790.0163052611393-0.03240683964860.0580620858908-0.0351456214919-0.05784738003650.1176407812730.06289706229790.11720376728220.505521306453.423972048831.1133710062
145.367918105952.14090441674-0.4357676843643.136272661120.73021327590.989183745291-0.5090781482490.8528559769170.0400804061681-0.5275733924520.5032417706040.6726747702370.367806118427-0.4760690944540.05343958654950.386793769596-0.2620714604640.06659938653360.381670939432-0.02617061472550.3764057224833.165772649450.350433648416.3459476676
155.12231717253-1.14921851414-2.264366568682.751048489462.16918633544.15621026487-0.0270359656723-0.3304553702740.09810188343990.07942031201330.12626948352-0.1128367820490.0349662863217-0.0587891371893-0.1066775643080.0830509136665-0.0577353166497-0.008121575165940.1349430449460.02157517357290.12040529934321.613718288451.870266686333.8632330522
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 9 )AA1 - 91 - 9
22chain 'A' and (resid 10 through 33 )AA10 - 3310 - 33
33chain 'A' and (resid 34 through 47 )AA34 - 4734 - 47
44chain 'A' and (resid 48 through 54 )AA48 - 5448 - 54
55chain 'A' and (resid 55 through 78 )AA55 - 7855 - 78
66chain 'A' and (resid 79 through 96 )AA79 - 9679 - 96
77chain 'B' and (resid 1 through 9 )BB1 - 91 - 9
88chain 'B' and (resid 10 through 26 )BB10 - 2610 - 26
99chain 'B' and (resid 27 through 33 )BB27 - 3327 - 33
1010chain 'B' and (resid 34 through 47 )BB34 - 4734 - 47
1111chain 'B' and (resid 48 through 54 )BB48 - 5448 - 54
1212chain 'B' and (resid 55 through 66 )BB55 - 6655 - 66
1313chain 'B' and (resid 67 through 78 )BB67 - 7867 - 78
1414chain 'B' and (resid 79 through 83 )BB79 - 8379 - 83
1515chain 'B' and (resid 84 through 96 )BB84 - 9684 - 96

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