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- PDB-6l4j: Monomer structure of monellin loop1 mutant (YEPKG) -

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Basic information

Entry
Database: PDB / ID: 6l4j
TitleMonomer structure of monellin loop1 mutant (YEPKG)
ComponentsSingle chain Monellin
KeywordsPLANT PROTEIN / Single chain Monellin / Loop1 mutant
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsManjula, R. / Ramaswamy, S. / Gosavi, S.
CitationJournal: To Be Published
Title: Monomer structure of Loop1 mutant Monellin with YEPKG motif
Authors: Manjula, R. / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,3392
Polymers21,3392
Non-polymers00
Water2,108117
1
A: Single chain Monellin


Theoretical massNumber of molelcules
Total (without water)10,6691
Polymers10,6691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Single chain Monellin


Theoretical massNumber of molelcules
Total (without water)10,6691
Polymers10,6691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.830, 64.250, 45.640
Angle α, β, γ (deg.)90.000, 102.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 2 - 91 / Label seq-ID: 2 - 91

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Single chain Monellin


Mass: 10669.255 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.: 117 / 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 YEPK.

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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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M carboxylic acid, 0.1M Imidazole, MES monohydrate

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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: May 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 2.3→36.58 Å / Num. obs: 7502 / % possible obs: 96.2 % / Redundancy: 3 % / CC1/2: 0.981 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.052 / Rrim(I) all: 0.091 / Net I/σ(I): 11.5 / Num. measured all: 22730 / Scaling rejects: 104
Reflection shell

Diffraction-ID: 1 / Redundancy: 3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.380.12223087690.9490.0830.1487100
8.91-36.580.0744261430.9710.0530.0911698.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9A

2o9a


Resolution: 2.3→36.579 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 22.51
RfactorNum. reflection% reflection
Rfree0.2386 385 5.14 %
Rwork0.1656 --
obs0.1691 7486 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.83 Å2 / Biso mean: 22.1933 Å2 / Biso min: 7.44 Å2
Refinement stepCycle: final / Resolution: 2.3→36.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 0 117 1607
Biso mean---26.62 -
Num. residues----180
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A548X-RAY DIFFRACTION10.224TORSIONAL
12B548X-RAY DIFFRACTION10.224TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3002-2.6330.27061420.19142432100
2.633-3.31690.271160.1845233095

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