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- PDB-7d75: X-ray structure of a domain-swapped dimer of Monellin with YEDKG ... -

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Basic information

Entry
Database: PDB / ID: 7d75
TitleX-ray structure of a domain-swapped dimer of Monellin with YEDKG loop-1 mutant
ComponentsSingle chain Monellin
KeywordsPLANT PROTEIN / X-ray crystal structure
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsManjula, R. / Ramaswamy, S. / Gosavi, S.
CitationJournal: To Be Published
Title: Domain swapped structure of Monellin Loop1-mutant
Authors: Manjula, R. / Gosavi, S. / Subramanian, R.
History
DepositionOct 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Structure summary / Category: entity / pdbx_entry_details / struct
Item: _entity.details / _pdbx_entry_details.sequence_details / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single chain Monellin
B: Single chain Monellin
C: Single chain Monellin
D: Single chain Monellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,73036
Polymers42,7494
Non-polymers1,98132
Water84747
1
A: Single chain Monellin
B: Single chain Monellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,77323
Polymers21,3742
Non-polymers1,39921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-128 kcal/mol
Surface area10640 Å2
MethodPISA
2
C: Single chain Monellin
D: Single chain Monellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,95613
Polymers21,3742
Non-polymers58211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-158 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.794, 55.783, 105.831
Angle α, β, γ (deg.)90.000, 93.630, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Single chain Monellin


Mass: 10687.228 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The complete sequence of single chain Monellin has been deposited to NCBI with accession code AFF58925. Residues 48-57 YENEGFREIK have been replaced with YEDK.
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6M Mg sulfate heptahydrate, 0.1M MES 6.5

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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 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→45.7 Å / Num. obs: 18428 / % possible obs: 98.9 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.047 / Rrim(I) all: 0.112 / Net I/σ(I): 7.7 / Num. measured all: 105391 / Scaling rejects: 102
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
2.5-2.65.70.6071115519580.9490.2730.6672.494
9.02-45.75.30.06321874160.9970.0280.06913.698.1

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L4J

6l4j


Resolution: 2.5→42.95 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 47.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3044 841 4.66 %
Rwork0.2619 17202 -
obs0.264 18043 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.25 Å2 / Biso mean: 42.9786 Å2 / Biso min: 18.57 Å2
Refinement stepCycle: final / Resolution: 2.5→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 102 47 3129
Biso mean--72.36 39 -
Num. residues----360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.660.4231560.39132795295195
2.66-2.860.38241290.34092889301898
2.86-3.150.33491490.30142913306299
3.15-3.610.28391340.2522884301897
3.61-4.540.28391390.22122839297896
4.55-42.950.26821340.22882882301695

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