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- PDB-5ycu: Domain swapped dimer of engineered hairpin loop1 mutant in Single... -

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Basic information

Entry
Database: PDB / ID: 5ycu
TitleDomain swapped dimer of engineered hairpin loop1 mutant 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


Helix Hairpins - #2000 / N-terminal domain of TfIIb - #130 / Monellin, B chain / Monellin / Monellin / N-terminal domain of TfIIb / Cystatin superfamily / Other non-globular / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsSurana, P. / Nandwani, N. / Udgaonkar, J.B. / Gosavi, S. / Das, R.
Funding support India, 1items
OrganizationGrant numberCountry
National Center for Biological Sciences India
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
B: Single chain monellin
C: Single chain monellin
D: Single chain monellin
E: Single chain monellin


Theoretical massNumber of molelcules
Total (without water)54,1675
Polymers54,1675
Non-polymers00
Water88349
1
A: Single chain monellin
B: Single chain monellin


Theoretical massNumber of molelcules
Total (without water)21,6672
Polymers21,6672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-37 kcal/mol
Surface area10720 Å2
MethodPISA
2
C: Single chain monellin
D: Single chain monellin


Theoretical massNumber of molelcules
Total (without water)21,6672
Polymers21,6672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-38 kcal/mol
Surface area10850 Å2
MethodPISA
3
E: Single chain monellin

E: Single chain monellin


Theoretical massNumber of molelcules
Total (without water)21,6672
Polymers21,6672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area4770 Å2
ΔGint-36 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.645, 86.301, 86.818
Angle α, β, γ (deg.)90.00, 127.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Single chain monellin


Mass: 10833.438 Da / Num. of mol.: 5 / Mutation: YENEGFREIK to QVVA
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.: 49 / 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 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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 8-12% (wt/vol) PEG 8000, 50mM sodium phosphate, pH 6.4-6.8
PH range: 6.4-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.32→43.15 Å / Num. obs: 26814 / % possible obs: 97.19 % / Redundancy: 3.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.038 / Net I/σ(I): 15.02
Reflection shellHighest resolution: 2.32 Å / Rmerge(I) obs: 0.924 / Mean I/σ(I) obs: 0.92 / CC1/2: 0.663 / % possible all: 91.51

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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: 2.32→43.15 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.02
RfactorNum. reflection% reflection
Rfree0.2701 1367 5.11 %
Rwork0.2394 --
obs0.2409 26752 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.32→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 0 49 3694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073734
X-RAY DIFFRACTIONf_angle_d1.265044
X-RAY DIFFRACTIONf_dihedral_angle_d14.0771424
X-RAY DIFFRACTIONf_chiral_restr0.069525
X-RAY DIFFRACTIONf_plane_restr0.008657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3203-2.40320.44771340.39542362X-RAY DIFFRACTION91
2.4032-2.49950.37071180.38422519X-RAY DIFFRACTION97
2.4995-2.61320.38551260.3812573X-RAY DIFFRACTION98
2.6132-2.7510.45291380.38162578X-RAY DIFFRACTION99
2.751-2.92330.35621350.36232598X-RAY DIFFRACTION99
2.9233-3.14890.34121410.32292586X-RAY DIFFRACTION99
3.1489-3.46570.32831470.3112544X-RAY DIFFRACTION97
3.4657-3.96690.31111450.25262466X-RAY DIFFRACTION95
3.9669-4.99670.21431600.1992530X-RAY DIFFRACTION97
4.9967-43.15790.21211230.17722629X-RAY DIFFRACTION97
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)
10.3565-0.130.12970.0912-0.3223-0.05810.13621.36120.74580.8151-0.1715-0.630.8235-1.6459-01.0502-0.04410.12210.67320.03040.9098-5.05589.8721-1.4491
2-0.07661.4794-0.7183-0.1285-0.1539-0.3118-0.2903-0.2028-0.21380.27940.35270.027-0.16260.2741-00.9593-0.05-0.04550.61530.00260.729-16.5728-3.14662.7107
31.3812-1.01880.33220.3152-0.7110.42770.2377-0.3023-0.3236-0.3808-0.20990.3617-0.00140.0695-00.9308-0.1101-0.01120.67960.00130.7433-10.2424-0.46764.3654
42.0010.620.30131.43571.09940.2769-0.34160.23830.6052-0.13570.52520.27470.33240.3649-00.7884-0.09240.00970.88930.21730.7679-8.159420.4055-36.3891
51.1736-0.1442-0.13330.88041.5931.8656-0.26670.21790.4595-0.05540.0179-0.07950.2313-0.735800.6728-0.0739-0.07451.08390.30341.0484-11.706221.1006-36.2705
60.38340.4223-0.04670.1273-0.34770.10530.7797-0.1051-0.14030.30750.0987-0.53011.35360.4261-00.68590.0544-0.07451.25990.14190.82290.186417.6767-31.828
7-0.83020.10770.62170.02660.64052.1491-0.45260.3892-0.0185-0.48030.67460.12690.5404-0.5659-00.5944-0.2424-0.1411.03350.3120.7266-12.059220.8176-44.7707
8-0.30781.48391.9451-0.127-0.9148-0.2624-0.25270.22470.0820.5672-0.1568-0.1814-0.1467-0.631-00.81330.22850.12670.70120.01380.6611-7.587811.5805-18.0907
91.0463-0.7474-0.65620.2139-0.46-0.74730.4823-0.0723-0.2425-0.361-0.10170.17930.01230.0501-00.9391-0.0748-0.08530.57810.05090.5857-10.4173-1.38931.5359
100.7589-0.0135-0.80690.7287-0.7775-0.63620.28840.2385-0.58340.0569-0.23520.2089-0.04440.0721-00.89440.0596-0.07860.6213-0.02980.8586-10.1633-3.3819-1.069
110.0763-0.08370.04730.22420.03950.0680.7712-0.2547-1.2989-0.63320.655-0.94590.2659-0.814900.8027-0.0584-0.08410.99980.04081.0866-44.539422.720733.401
121.02111.0580.23190.05280.66021.3061-0.3754-0.430.04940.39630.6936-0.9486-0.3039-0.1901-00.5953-0.0019-0.04150.8892-0.12230.8448-40.790837.442144.4984
130.41480.4710.3104-0.25250.23710.50440.0239-0.0920.04760.3020.0143-0.4156-0.3469-0.6601-00.83060.1274-0.0250.9670.01760.8766-46.547936.301548.2358
140.2238-0.34610.5242-0.2782-0.69680.2274-0.00510.2327-0.5904-0.13840.3653-0.13250.639-0.180900.7332-0.02590.05910.7728-0.05210.8404-40.009926.552726.8114
151.785-0.19630.06281.3537-0.2927-0.28950.2716-0.0947-0.1151-0.2912-0.434-0.0066-0.25410.121-00.9950.01980.05530.598-0.04760.6845-31.042715.62071.836
161.4368-0.23652.26141.6680.8391.15890.3792-0.17880.3669-0.245-0.12620.0637-0.0769-0.032200.96880.0410.09020.5520.02150.7787-31.972717.8691-1.8302
170.46610.74580.6416-0.18410.6790.18830.6464-0.0807-0.34-0.1165-0.75040.3052-1.37440.5237-00.88470.0105-0.02670.76510.03140.8534-37.942712.7718-2.4145
180.64220.4968-0.0666-0.4233-0.0470.28570.0331-0.00370.6591-0.6503-0.0205-0.0587-0.3869-0.1232-00.7534-0.02040.03350.7924-0.01350.7853-36.052425.017323.1129
19-0.0336-0.66510.31160.6278-0.08110.67080.1096-0.41390.1110.21470.1793-0.1188-0.0922-0.2673-00.48950.01020.05870.9922-0.05460.6853-47.365235.163542.6718
200.28361.3905-0.14491.76530.89920.9821-0.20580.69440.048-0.31580.60420.08760.3056-0.0495-00.6144-0.0746-0.00190.9018-0.02930.8672-42.480935.703736.9742
210.02-0.0618-0.0457-0.02810.0716-0.0030.8463-0.4291-0.0785-0.1092-0.2591.1112-0.465-0.498800.9307-0.04860.0731.3338-0.05221.275-45.58925.01449.9048
22-0.35250.68450.03771.4656-0.7517-0.6484-0.4961-1.1306-0.173-0.03610.38740.36620.48480.1366-01.08830.21610.06291.61680.26741.0585-34.0542-5.973421.0605
230.04452.0045-1.1913-0.4923-1.26361.3667-0.0648-0.44470.1626-0.0869-0.49160.14580.1155-0.170200.92910.0863-0.13671.1416-0.13580.9649-52.3667-0.26011.756
240.43091.0508-0.03341.62621.68521.06870.16490.8644-1.2086-0.1312-0.51240.1950.1971-1.3854-00.7505-0.1213-0.08561.9721-0.51211.0035-73.6802-1.7908-15.7949
250.82950.97460.67050.12150.8394-0.4675-0.3508-0.80970.1804-0.59620.2935-0.4890.568-0.753201.3992-0.1925-0.15491.5286-0.2271.206-72.9937-4.5032-12.277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:9)
2X-RAY DIFFRACTION2(chain A and resid 10:29)
3X-RAY DIFFRACTION3(chain A and resid 30:47)
4X-RAY DIFFRACTION4(chain A and resid 48:64)
5X-RAY DIFFRACTION5(chain A and resid 65:91)
6X-RAY DIFFRACTION6(chain B and resid 3:8)
7X-RAY DIFFRACTION7(chain B and resid 9:41)
8X-RAY DIFFRACTION8(chain B and resid 42:56)
9X-RAY DIFFRACTION9(chain B and resid 57:75)
10X-RAY DIFFRACTION10(chain B and resid 76:91)
11X-RAY DIFFRACTION11(chain C and resid 2:7)
12X-RAY DIFFRACTION12(chain C and resid 8:29)
13X-RAY DIFFRACTION13(chain C and resid 30:42)
14X-RAY DIFFRACTION14(chain C and resid 43:51)
15X-RAY DIFFRACTION15(chain C and resid 52:91)
16X-RAY DIFFRACTION16(chain D and resid 3:33)
17X-RAY DIFFRACTION17(chain D and resid 34:44)
18X-RAY DIFFRACTION18(chain D and resid 45:54)
19X-RAY DIFFRACTION19(chain D and resid 55:72)
20X-RAY DIFFRACTION20(chain D and resid 73:91)
21X-RAY DIFFRACTION21(chain E and resid 2:8)
22X-RAY DIFFRACTION22(chain E and resid 9:39)
23X-RAY DIFFRACTION23(chain E and resid 40:56)
24X-RAY DIFFRACTION24(chain E and resid 57:74)
25X-RAY DIFFRACTION25(chain E and resid 75:91)

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