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- PDB-6lay: Domain-swapped dimer structure of a Single-chain Monellin loop1-d... -

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Basic information

Entry
Database: PDB / ID: 6lay
TitleDomain-swapped dimer structure of a Single-chain Monellin loop1-delta4-QVVAG mutant
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / Monomer / L1 mutant
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 / molecular replacement / Resolution: 3.001 Å
AuthorsManjula, R. / Subramanian, R. / Gosavi, S.
CitationJournal: To Be Published
Title: Domain-swapped dimer structure of a Single-chain Monellin loop1-delta4-QVVAG mutant
Authors: Manjula, R. / Subramanian, R. / Gosavi, S.
History
DepositionNov 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)21,6812
Polymers21,6812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-39 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.170, 73.790, 45.990
Angle α, β, γ (deg.)90.000, 100.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 10840.429 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Monellin chain B, LINKER and Monellin chain A
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli (E. coli) / References: UniProt: P02882, UniProt: P02881

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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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 3350, 0.2mM sodium acetate ,Tris HCl pH 8.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5478 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 3→45.29 Å / Num. obs: 4033 / % possible obs: 100 % / Redundancy: 5.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.047 / Rrim(I) all: 0.109 / Net I/σ(I): 12.5 / Num. measured all: 21231 / Scaling rejects: 6
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
3-3.185.30.25333836410.9430.1220.2825.9100
9-45.294.90.0467991630.9980.0230.05121.499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9U

2o9u


Resolution: 3.001→45.289 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 192 4.78 %RANDOM
Rwork0.2074 3828 --
obs0.2099 4020 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.47 Å2 / Biso mean: 32.272 Å2 / Biso min: 21.7 Å2
Refinement stepCycle: final / Resolution: 3.001→45.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 0 0 1514
Num. residues----184
LS refinement shellResolution: 3.001→3.18 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2627 192 -
Rwork0.2074 3828 -
obs--100 %

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