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- PDB-6l44: Monomeric structure of monellin loop1 mutant with QVPAG motif -

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Basic information

Entry
Database: PDB / ID: 6l44
TitleMonomeric structure of monellin loop1 mutant with QVPAG motif
ComponentsSingle chain Monellin
KeywordsPLANT PROTEIN / Loop1 mutation / Monellin
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.492 Å
AuthorsManjula, R. / Ramaswamy, S. / Gosavi, S.
CitationJournal: To Be Published
Title: The monomer structure of Monellin Loop1 mutant
Authors: Manjula, R. / Gosavi, S. / Ramaswamy, S.
History
DepositionOct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5737
Polymers21,0922
Non-polymers4805
Water25214
1
A: Single chain Monellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6422
Polymers10,5461
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5690 Å2
MethodPISA
2
B: Single chain Monellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9305
Polymers10,5461
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area5600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.480, 30.041, 46.450
Angle α, β, γ (deg.)93.060, 100.280, 94.720
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 21 or resid 23...
21(chain B and ((resid 2 and (name CA or name...

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
11GLYGLYVALVAL(chain A and (resid 1 through 20 or resid 22...AA2 - 212 - 21
12GLUGLUASPASP(chain A and (resid 1 through 20 or resid 22...AA23 - 7323 - 73
13LYSLYSLEULEU(chain A and (resid 1 through 20 or resid 22...AA75 - 8275 - 82
14PHEPHEPROPRO(chain A and (resid 1 through 20 or resid 22...AA84 - 9184 - 91
21GLYGLYVALVAL(chain B and ((resid 1 and (name CA or name...BB2 - 212 - 21
22GLUGLUASPASP(chain B and ((resid 1 and (name CA or name...BB23 - 7323 - 73
23LYSLYSLEULEU(chain B and ((resid 1 and (name CA or name...BB75 - 8275 - 82
24PHEPHEPROPRO(chain B and ((resid 1 and (name CA or name...BB84 - 9184 - 91

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Components

#1: Protein Single chain Monellin


Mass: 10546.125 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 QVPA.

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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: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Sulfate, 0.1M Sodium cacodylate pH. 6.5, 30% PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.578 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.578 Å / Relative weight: 1
ReflectionResolution: 2.49→45.594 Å / Num. obs: 5238 / % possible obs: 96.3 % / Redundancy: 1.9 % / CC1/2: 0.975 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.058 / Rrim(I) all: 0.082 / Net I/σ(I): 8.3
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
2.49-2.591.90.14710325380.9160.1470.2083.791.3
8.99-45.5920.042281160.9850.040.0561299.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9A

2o9a


Resolution: 2.492→45.594 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 2.12 / Phase error: 14.88
RfactorNum. reflection% reflection
Rfree0.2501 261 4.98 %
Rwork0.1652 --
obs0.1699 5236 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.78 Å2 / Biso mean: 40.2876 Å2 / Biso min: 19.6 Å2
Refinement stepCycle: final / Resolution: 2.492→45.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1471 0 25 14 1510
Biso mean--68.45 37.12 -
Num. residues----180
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A795X-RAY DIFFRACTION13.568TORSIONAL
12B795X-RAY DIFFRACTION13.568TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4924-3.14010.37141240.1786244895
3.1401-8.990.21061370.16252798

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