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- PDB-7vww: X-ray structure of a domain-swapped poly-glutamine Monellin mutant -

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Basic information

Entry
Database: PDB / ID: 7vww
TitleX-ray structure of a domain-swapped poly-glutamine Monellin mutant
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / X-ray crystal structure
Function / homologyMonellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / Cystatin superfamily / DI(HYDROXYETHYL)ETHER / Monellin chain A / Monellin chain B
Function and homology information
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsManjula, R. / Ramaswamy, S. / Gosavi, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Effect of polyQ on protein assembly
Authors: Manjula, R. / Gosavi, S. / Subramanian, R.
History
DepositionNov 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monellin chain B,Monellin chain A
B: Monellin chain B,Monellin chain A
C: Monellin chain B,Monellin chain A
D: Monellin chain B,Monellin chain A
E: Monellin chain B,Monellin chain A
F: Monellin chain B,Monellin chain A
G: Monellin chain B,Monellin chain A
H: Monellin chain B,Monellin chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,80332
Polymers84,2568
Non-polymers2,54724
Water1,20767
1
A: Monellin chain B,Monellin chain A
B: Monellin chain B,Monellin chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8079
Polymers21,0642
Non-polymers7437
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-29 kcal/mol
Surface area11530 Å2
MethodPISA
2
C: Monellin chain B,Monellin chain A
D: Monellin chain B,Monellin chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,01911
Polymers21,0642
Non-polymers9559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-29 kcal/mol
Surface area11230 Å2
MethodPISA
3
E: Monellin chain B,Monellin chain A
F: Monellin chain B,Monellin chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5957
Polymers21,0642
Non-polymers5315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-25 kcal/mol
Surface area10900 Å2
MethodPISA
4
G: Monellin chain B,Monellin chain A
H: Monellin chain B,Monellin chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3825
Polymers21,0642
Non-polymers3183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-28 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.309, 68.149, 84.870
Angle α, β, γ (deg.)90.00, 92.66, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 10531.993 Da / Num. of mol.: 8 / Mutation: R48Q,E49Q,I50Q,K51Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli (E. coli) / References: UniProt: P02882, UniProt: P02881
#2: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Carboxylic acid, 0.1M Buffer system-2 pH7.5, 50% of precipitation mix-1 condition of Morpheus complete HT-96

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→53.12 Å / Num. obs: 26343 / % possible obs: 99.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 47.02 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.067 / Rrim(I) all: 0.095 / Net I/σ(I): 7.7 / Num. measured all: 50642
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.8320.397684335060.6820.3970.5611.6100
8.96-53.121.80.0213787620.9990.020.02917.899.3

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EUA

7eua


Resolution: 2.7→45.37 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3241 1228 4.72 %
Rwork0.2629 --
obs0.2657 26035 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→45.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5741 0 168 67 5976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026043
X-RAY DIFFRACTIONf_angle_d0.3578098
X-RAY DIFFRACTIONf_dihedral_angle_d25.331892
X-RAY DIFFRACTIONf_chiral_restr0.041820
X-RAY DIFFRACTIONf_plane_restr0.0021055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.810.36721400.32542761X-RAY DIFFRACTION100
2.81-2.940.34921480.28922748X-RAY DIFFRACTION100
2.94-3.090.28941140.27922804X-RAY DIFFRACTION100
3.09-3.280.34411600.28972723X-RAY DIFFRACTION100
3.28-3.540.48821180.34552687X-RAY DIFFRACTION96
3.54-3.890.32731200.30612696X-RAY DIFFRACTION96
3.89-4.460.30421220.23352758X-RAY DIFFRACTION98
4.46-5.610.27511430.20392802X-RAY DIFFRACTION100
5.61-45.370.29221630.23132828X-RAY DIFFRACTION99

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