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- PDB-5yct: Engineered hairpin loop3 mutant monomer in Single-chain Monellin -

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Basic information

Entry
Database: PDB / ID: 5yct
TitleEngineered hairpin loop3 mutant monomer in Single-chain Monellin
ComponentsSingle chain Monellin
KeywordsPLANT PROTEIN / domain swapped dimer / Single-chain Monellin / loop mutation / QVVAG motif
Function / homology
Function and homology information


Monellin, B chain / : / Monellin / Monellin / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.851 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

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Assembly

Deposited unit
A: Single chain Monellin
B: Single chain Monellin


Theoretical massNumber of molelcules
Total (without water)22,9862
Polymers22,9862
Non-polymers00
Water2,774154
1
A: Single chain Monellin


Theoretical massNumber of molelcules
Total (without water)11,4931
Polymers11,4931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Single chain Monellin


Theoretical massNumber of molelcules
Total (without water)11,4931
Polymers11,4931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.601, 48.103, 62.712
Angle α, β, γ (deg.)90.00, 103.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Single chain Monellin


Mass: 11493.126 Da / Num. of mol.: 2 / Mutation: 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


Mass: 18.015 Da / Num. of mol.: 154 / 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 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 8-12% (wt/vol) PEG 8000, 50mM sodium phosphate, pH 6.4-7.2, Crystals grew to maximum size in 4-5 days
PH range: 6.4-7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.851→24.052 Å / Num. obs: 17514 / % possible obs: 98.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.017 / Net I/σ(I): 24
Reflection shellHighest resolution: 1.851 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.1 / CC1/2: 0.924 / % possible all: 89.04

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IV7

1iv7


Resolution: 1.851→24.052 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.93
RfactorNum. reflection% reflection
Rfree0.2271 887 5.06 %
Rwork0.1922 --
obs0.1939 17513 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.851→24.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 0 154 1677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061559
X-RAY DIFFRACTIONf_angle_d1.1872101
X-RAY DIFFRACTIONf_dihedral_angle_d13.945598
X-RAY DIFFRACTIONf_chiral_restr0.052214
X-RAY DIFFRACTIONf_plane_restr0.005276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.851-1.96660.32141290.25592590X-RAY DIFFRACTION93
1.9666-2.11840.25971700.22142750X-RAY DIFFRACTION100
2.1184-2.33140.2371440.20492797X-RAY DIFFRACTION100
2.3314-2.66840.2571410.20662814X-RAY DIFFRACTION100
2.40535-3.36040.1941370.17062885X-RAY DIFFRACTION100
2.6684-3.36040.23931660.20392790X-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)
10.7353-0.523-0.23551.68380.45941.3639-0.0522-0.10090.10330.12140.0112-0.0222-0.01960.1264-00.19890.00090.00190.25760.00470.240636.61850.043727.5319
20.4690.20940.0331.102-0.4821.218-0.05570.03050.0027-0.05130.13120.2079-0.1126-0.216300.3167-0.0011-0.03630.25940.02320.243830.61851.2935.1631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:97)
2X-RAY DIFFRACTION2(chain B and resid 2:97)

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