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- PDB-8tm8: Monomer structure of monellin loop1 mutant (YENKG) -

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Basic information

Entry
Database: PDB / ID: 8tm8
TitleMonomer structure of monellin loop1 mutant (YENKG)
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / single-chain Monellin / Sweet protein / domain swapping
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 / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsManjula, R. / Pavithra, G.C. / Ramaswamy, S. / Gosavi, S.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Monomer structure of monellin loop1 mutant (YENKG)
Authors: Pavithra, G.C. / Manjula, R. / Ramaswamy, S. / Gosavi, S.
History
DepositionJul 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,4184
Polymers21,3722
Non-polymers462
Water99155
1
A: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)10,6861
Polymers10,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monellin chain B,Monellin chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7323
Polymers10,6861
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.139, 58.789, 45.210
Angle α, β, γ (deg.)90.00, 91.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 10686.243 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02882, UniProt: P02881
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.81 Å3/Da / Density % sol: 32.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 2.0M Ammonium sulfate, 0.2M potassium sodium tartarate tetrahydrate, 0.1M sodium citrate pH5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→45.18 Å / Num. obs: 7206 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.997 / Net I/σ(I): 17.4
Reflection shellResolution: 2.26→2.33 Å / Num. unique obs: 7206 / CC1/2: 0.985 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→45.18 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 722 10.09 %
Rwork0.1916 --
obs0.1986 7153 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 2 55 1484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041480
X-RAY DIFFRACTIONf_angle_d0.7682000
X-RAY DIFFRACTIONf_dihedral_angle_d14.217203
X-RAY DIFFRACTIONf_chiral_restr0.049203
X-RAY DIFFRACTIONf_plane_restr0.005264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.430.35791410.22531234X-RAY DIFFRACTION96
2.43-2.680.30361460.22761290X-RAY DIFFRACTION100
2.68-3.060.27311410.20861274X-RAY DIFFRACTION100
3.07-3.860.25791450.17991308X-RAY DIFFRACTION100
3.86-45.180.21431490.16981325X-RAY DIFFRACTION100

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