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- PDB-9hij: X-ray structure of Perm1, a circularly permuted mutant of the swe... -

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Basic information

Entry
Database: PDB / ID: 9hij
TitleX-ray structure of Perm1, a circularly permuted mutant of the sweet protein MNEI
ComponentsMonellin chain A,Monellin chain B
KeywordsPLANT PROTEIN / sweet protein
Function / homology
Function and homology information


Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / Cystatin superfamily
Similarity search - Domain/homology
ACETATE ION / Monellin chain A / Monellin chain B
Similarity search - Component
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBologna, A. / Wang, P.-H. / Gramazio, S. / Essen, L.-O. / Spadaccini, R.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other government Italy
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Unravelling the amyloid aggregation mechanism of the sweet protein Monellin: Insights from circular permutated mutants.
Authors: Lucignano, R. / Bologna, A. / Gramazio, S. / Wang, P.H. / Taxis, C. / Essen, L.O. / Picone, D. / Spadaccini, R.
History
DepositionNov 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,8386
Polymers23,3552
Non-polymers4844
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-50 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.646, 31.599, 127.006
Angle α, β, γ (deg.)90.000, 100.200, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 or resid 6 through 13...
d_2ens_1(chain "B" and ((resid 4 and (name N or name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUGLUGLUAA44
d_12LYSLYSTYRTYRAA6 - 136 - 13
d_13TYRTYRILEILEAA15 - 2515 - 25
d_14GLUGLUPROPROAA27 - 9127 - 91
d_15LYSLYSGLUGLUAA94 - 9994 - 99
d_21GLUGLUGLUGLUBB44
d_22LYSLYSTYRTYRBB6 - 136 - 13
d_23TYRTYRILEILEBB15 - 2515 - 25
d_24GLUGLUPROPROBB27 - 9127 - 91
d_25LYSLYSGLUGLUBB94 - 9994 - 99

NCS oper: (Code: givenMatrix: (-0.977178953865, 0.210738455841, 0.0266569944582), (0.206682518998, 0.914314573076, 0.348297570766), (0.049026813729, 0.345858590598, -0.937004912925)Vector: 17. ...NCS oper: (Code: given
Matrix: (-0.977178953865, 0.210738455841, 0.0266569944582), (0.206682518998, 0.914314573076, 0.348297570766), (0.049026813729, 0.345858590598, -0.937004912925)
Vector: 17.1104858459, -17.3161419983, 85.8149092026)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 11677.284 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli B (bacteria) / References: UniProt: P02881, UniProt: P02882

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Non-polymers , 5 types, 86 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.93 Å3/Da / Density % sol: 36.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Precipitant: 25% (w/v) PEG1000, 25% (w/v) PEG3350 and 25% (v/v) (RS)-2-methyl-2,4-pentanediol (MPD) Buffer: 0.1 M Tris (base); BICINE (pH 8.5) Divalents: 0.3 M Magnesium chloride ...Details: Precipitant: 25% (w/v) PEG1000, 25% (w/v) PEG3350 and 25% (v/v) (RS)-2-methyl-2,4-pentanediol (MPD) Buffer: 0.1 M Tris (base); BICINE (pH 8.5) Divalents: 0.3 M Magnesium chloride hexahydrate, 0.3 M Calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2021
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40.08 Å / Num. obs: 23048 / % possible obs: 96.29 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.15 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0539 / Rpim(I) all: 0.0344 / Rrim(I) all: 0.0642 / Net I/σ(I): 12.68
Reflection shellResolution: 1.6→1.67 Å / Rmerge(I) obs: 0.7828 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 2809 / CC1/2: 0.627 / CC star: 0.878 / Rpim(I) all: 0.5167 / Rrim(I) all: 0.9433 / % possible all: 94.55

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→40.08 Å / SU ML: 0.2018 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1905 1177 5.11 %
Rwork0.1706 21871 -
obs0.1717 23048 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 32 82 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761658
X-RAY DIFFRACTIONf_angle_d1.06932234
X-RAY DIFFRACTIONf_chiral_restr0.0557224
X-RAY DIFFRACTIONf_plane_restr0.0137290
X-RAY DIFFRACTIONf_dihedral_angle_d13.8061645
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.908190771865 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.670.30811590.27582650X-RAY DIFFRACTION94.55
1.67-1.760.26071430.22242774X-RAY DIFFRACTION98.25
1.76-1.870.24381420.21452765X-RAY DIFFRACTION98.18
1.87-2.020.20821320.1672709X-RAY DIFFRACTION96.73
2.02-2.220.18951450.16042757X-RAY DIFFRACTION97.28
2.22-2.540.18871450.16542764X-RAY DIFFRACTION96.93
2.54-3.20.2051530.16892721X-RAY DIFFRACTION95.64
3.2-40.080.1671580.1612731X-RAY DIFFRACTION93.13
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)
12.24980893689-0.315598575412-0.6103743547983.648354504912.94530640775.014230615040.03838994297760.441554015607-0.286574654133-0.4035001291160.149481214133-0.2447771121020.06881654790820.389188981966-0.2127600778690.2556268503040.02544615166830.02295390503730.321399044322-0.04379141824540.26061715125620.302442416410.164003771246.154356147
23.10131567290.407266927293-0.2692406264852.052537950.6944078534243.838168352030.07459125424210.373958293674-0.251062150083-0.163108276920.0194298317858-0.5798557985570.1606465749850.0655856824892-0.0830616096090.2245040221450.01087941174250.019917946350.217653104332-0.009686535638820.32349247097523.924271682712.20711262947.656964967
32.61378182610.1721060558250.02844678589051.070818644370.3492317473880.588148219870.03338128991140.01452344988560.0758089816028-0.0343300596984-0.0330152009255-0.03017951479690.07741579843420.05360971753440.008609714765310.2506470524560.007526381544540.00648190510720.2442748737370.01913379860490.19158230328111.947317782212.819157693448.5454129229
42.24832676564-0.647722130197-0.6132403926237.708273319992.740838018432.94233771085-0.00438864846895-0.009941612825470.0341132343161-0.372391500045-0.1884717980020.711199179616-0.0894539478005-0.2545610360770.1683490074640.2811737518190.0187759716052-0.05404984609280.240293079309-0.00828591303680.278231275119-4.9964122275419.392761900941.7108068032
52.154468941190.174212230365-0.3017248247394.12500190149-0.2701225117481.47434799145-0.00920585739474-0.0944761886487-0.173362791416-0.3566433229840.0252989813431-0.03133018736290.1577898644140.0392210450469-0.02736109568630.1640302656160.0191452399188-0.02973634555290.225923079571-0.01174322019570.1643808820791.4735448868715.092080522144.6241147804
63.394601834240.743543044243-1.026031604113.50331171342-1.179140415912.61404880332-0.00280661944398-0.229592518281-0.255702159610.0242608958093-0.05347402521110.0460043733850.08397552232310.1069225992040.08785417390510.1989550362890.0152250176613-0.006590155538540.218285197142-0.004119692849070.1934964045690.18109068412611.124465570447.5848987425
72.91203112830.132942648964-0.2172545541631.05963821683-0.06865070873761.6522277923-0.0347812688228-0.251267442946-0.161357095212-0.0746702925586-0.09500888415140.146594451096-0.07953950234410.04269080588740.1300890309940.1864505270610.03439970047820.004377490572190.174374760166-0.01590554591120.209626910167-2.5003554687815.301323151546.9913560126
82.57785448388-1.029999188770.08363628695853.28459481643-0.02607484516210.9156383721950.09901816234310.12560731092-0.0181024602359-0.318647500913-0.0838772304104-0.00545172435774-0.00327586587226-0.0345110477527-0.006862891108570.233192523901-0.01457669162610.006084188017670.1877571878920.0002201690206340.1448769337119.4425379575613.783725835345.1709355493
95.210669258341.24550633155-0.3708386889915.893729664591.112840468063.950057241340.1172922819890.1690845574430.1907133904250.002121436788850.230813940111-0.26490268619-0.2004990932230.313946437427-0.3015635311380.165073125380.003765917908630.02254950030080.225975620156-0.009107745403730.23611239346627.136486957413.926216670553.1402408739
102.4361471657-0.0839658027738-0.06709640261721.811584969840.3296634558623.591039832170.07985531302990.195016448069-0.0272699896332-0.1254686292570.0616193615412-0.139620961301-0.167361497150.0979771927493-0.08558036300850.1933386179670.01020965226970.01878743790290.259763856084-0.01677132801970.22655188840520.100644365213.021672291850.9472513986
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 16 )AA4 - 161 - 13
22chain 'A' and (resid 17 through 33 )AA17 - 3314 - 30
33chain 'A' and (resid 34 through 60 )AA34 - 6031 - 57
44chain 'A' and (resid 61 through 77 )AA61 - 7758 - 74
55chain 'A' and (resid 78 through 100 )AA78 - 10075 - 97
66chain 'B' and (resid 4 through 16 )BC4 - 161 - 13
77chain 'B' and (resid 17 through 33)BC17 - 3314 - 30
88chain 'B' and (resid 34 through 60 )BC34 - 6031 - 57
99chain 'B' and (resid 61 through 77 )BC61 - 7758 - 74
1010chain 'B' and (resid 78 through 99 )BC78 - 9975 - 96

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