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- PDB-5ycw: Double domain swapped dimer of engineered hairpin loop1 and loop3... -

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Basic information

Entry
Database: PDB / ID: 5ycw
TitleDouble domain swapped dimer of engineered hairpin loop1 and loop3 mutant in Single-chain Monellin
Componentssingle chain monellin
KeywordsPLANT PROTEIN / domain swapped dimer / Single-chain Monellin / loop mutation / QVVAG motif
Function / homologyMonellin, B chain / Monellin / Monellin / Cystatin superfamily / Monellin chain B
Function and homology information
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.285 Å
AuthorsSurana, P. / Nandwani, N. / Udgaonkar, J.B. / Gosavi, S. / Das, R.
CitationJournal: Nat Commun / Year: 2019
Title: A five-residue motif for the design of domain swapping in proteins.
Authors: Nandwani, N. / Surana, P. / Negi, H. / Mascarenhas, N.M. / Udgaonkar, J.B. / Das, R. / Gosavi, S.
History
DepositionSep 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: single chain monellin


Theoretical massNumber of molelcules
Total (without water)10,6221
Polymers10,6221
Non-polymers00
Water724
1
A: single chain monellin

A: single chain monellin


Theoretical massNumber of molelcules
Total (without water)21,2442
Polymers21,2442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6270 Å2
ΔGint-42 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.110, 48.110, 103.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein single chain monellin


Mass: 10622.219 Da / Num. of mol.: 1
Mutation: YENEGFREIK to QVVA in loop1, DYKTR to QVVAG in loop3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli (E. coli) / References: UniProt: P02882*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe complete sequence of single chain Monellin has been deposited to NCBI with accession code ...The complete sequence of single chain Monellin has been deposited to NCBI with accession code AFF58925. Residues 48-57 YENEGFREIK have been replaced with QVVA, Residues 79-83 DYKTR have been replaced with QVVAG in this structure. C-terminal residues STP are from expression tag.

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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: 3.25 Å3/Da / Density % sol: 62.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 8-12% (wt/vol) PEG 8000, 50mM sodium phosphate, pH 6.4-6.8, Crystals grew in a week
PH range: 6.4-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.285→41.66 Å / Num. obs: 6521 / % possible obs: 97.28 % / Redundancy: 5.9 % / Biso Wilson estimate: 71.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03691 / Net I/σ(I): 22.76
Reflection shellHighest resolution: 2.285 Å / Rmerge(I) obs: 0.7052 / Mean I/σ(I) obs: 2.46 / CC1/2: 0.85 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IV7

1iv7


Resolution: 2.285→41.66 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.91
RfactorNum. reflection% reflection
Rfree0.2633 646 9.91 %
Rwork0.222 --
obs0.2263 6520 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.285→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 0 4 724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006737
X-RAY DIFFRACTIONf_angle_d1.047996
X-RAY DIFFRACTIONf_dihedral_angle_d14.575279
X-RAY DIFFRACTIONf_chiral_restr0.04105
X-RAY DIFFRACTIONf_plane_restr0.008130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2849-2.46130.43021270.38371165X-RAY DIFFRACTION100
2.4613-2.70890.38241160.35771038X-RAY DIFFRACTION88
2.7089-3.10080.38821270.30741182X-RAY DIFFRACTION100
3.1008-3.90620.29321400.24611198X-RAY DIFFRACTION99
3.9062-41.67140.20731360.17751291X-RAY DIFFRACTION100
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)
10.8792-0.4036-0.29721.0839-0.41332.2506-0.13750.0563-0.4594-0.00770.40330.3522-0.269-0.2086-00.49110.08380.04660.58040.00150.7136-3.270819.5334-0.9586
20.1053-0.118-0.44710.34330.0987-0.4193-0.8822-0.10370.51340.59040.6124-0.1953-0.5074-0.091901.29540.16760.10060.62290.06441.009-0.516838.0568-0.066
31.8579-0.4471-0.69141.3353-0.8340.96940.01480.09920.15260.0934-0.0251-0.1503-0.20770.067300.59840.0971-0.01470.6614-0.02790.5284-0.787220.57260.8379
42.4429-2.01030.46313.5193-0.70020.0323-0.04350.4039-0.2120.2853-0.17070.11350.0648-0.4134-00.55220.02840.07450.51820.01870.4519-21.075411.153433.7663
51.5313-2.22071.52971.52-2.78690.759-0.13850.2884-0.16520.5027-0.0315-0.6135-0.4528-0.30100.8463-0.01570.02250.7788-0.06930.87072.337226.62211.7848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:23)
2X-RAY DIFFRACTION2(chain A and resid 24:31)
3X-RAY DIFFRACTION3(chain A and resid 32:52)
4X-RAY DIFFRACTION4(chain A and resid 53:75)
5X-RAY DIFFRACTION5(chain A and resid 76:91)

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