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- PDB-6l4i: Monomeric structure of monellin loop1 mutant with QEPKG motif -

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Basic information

Entry
Database: PDB / ID: 6l4i
TitleMonomeric structure of monellin loop1 mutant with QEPKG motif
ComponentsSingle chain Monellin
KeywordsPLANT PROTEIN / Monomer / L1 mutant
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsManjula, R. / Ramaswamy, S. / Gosavi, S.
CitationJournal: To Be Published
Title: Monomer structure of Loop1 mutant Monellin with QEPKG motif
Authors: Manjula, R. / Ramaswamy, S. / Gosavi, S.
History
DepositionOct 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,2682
Polymers21,2682
Non-polymers00
Water1,08160
1
A: Single chain Monellin


Theoretical massNumber of molelcules
Total (without water)10,6341
Polymers10,6341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Single chain Monellin


Theoretical massNumber of molelcules
Total (without water)10,6341
Polymers10,6341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.049, 58.322, 45.183
Angle α, β, γ (deg.)90.000, 91.990, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 33 or resid 35...
21(chain B and (resid 2 through 33 or resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEU(chain A and (resid 1 through 32 or resid 34...AA2 - 332 - 33
12PHEPHETHRTHR(chain A and (resid 1 through 32 or resid 34...AA35 - 4635 - 46
13GLYGLYPHEPHE(chain A and (resid 1 through 32 or resid 34...AA52 - 8452 - 84
14GLYGLYPROPRO(chain A and (resid 1 through 32 or resid 34...AA86 - 9186 - 91
21GLYGLYLEULEU(chain B and (resid 1 through 32 or resid 34...BB2 - 332 - 33
22PHEPHETHRTHR(chain B and (resid 1 through 32 or resid 34...BB35 - 4635 - 46
23GLYGLYLYSLYS(chain B and (resid 1 through 32 or resid 34...BB52 - 7552 - 75
24ARGARGASNASN(chain B and (resid 1 through 32 or resid 34...BB77 - 8577 - 85
25GLYGLYPROPRO(chain B and (resid 1 through 32 or resid 34...BB86 - 9186 - 91

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Components

#1: Protein Single chain Monellin


Mass: 10634.210 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)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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 QEPK.

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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: 1.8 Å3/Da / Density % sol: 31.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.1 / Details: 20% PEG 3350, 0.2M Ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.548 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.548 Å / Relative weight: 1
ReflectionResolution: 2.2→45.16 Å / Num. obs: 7620 / % possible obs: 98.6 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.026 / Rrim(I) all: 0.059 / Net I/σ(I): 21.8 / Num. measured all: 37427 / Scaling rejects: 89
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
2.2-2.273.90.11823386060.9920.0660.13611.491.1
9.07-45.164.60.0415381160.9990.0220.04729.798.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.152refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9A

2o9a


Resolution: 2.2→35.705 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 28.34
RfactorNum. reflection% reflection
Rfree0.2471 396 5.2 %
Rwork0.178 --
obs0.1816 7619 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.07 Å2 / Biso mean: 24.6482 Å2 / Biso min: 9.44 Å2
Refinement stepCycle: final / Resolution: 2.2→35.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 0 60 1498
Biso mean---27.32 -
Num. residues----175
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A474X-RAY DIFFRACTION8.591TORSIONAL
12B474X-RAY DIFFRACTION8.591TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2001-2.51840.31011180.2051234596
2.5184-3.17270.29141380.1992413100

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