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- PDB-5xfu: Domain swapped dimer crystal structure of loop1 deletion mutant i... -

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Basic information

Entry
Database: PDB / ID: 5xfu
TitleDomain swapped dimer crystal structure of loop1 deletion mutant in Single-chain Monellin
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / domain swapped dimer / Single-chain Monellin / hinge loop composition / loop deletion
Function / homology
Function and homology information


Helix Hairpins - #2000 / N-terminal domain of TfIIb - #130 / Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / N-terminal domain of TfIIb / Cystatin superfamily / Other non-globular ...Helix Hairpins - #2000 / N-terminal domain of TfIIb - #130 / Monellin, A chain / Monellin, A chain superfamily / 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
Monellin chain A / Monellin chain B
Similarity search - Component
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.611 Å
AuthorsSurana, P. / Nandwani, N. / Udgaonkar, J. / Gosavi, S. / Das, R.
Funding support India, 1items
OrganizationGrant numberCountry
TIFR-DAE India
CitationJournal: Protein Sci. / Year: 2017
Title: Amino-acid composition after loop deletion drives domain swapping
Authors: Nandwani, N. / Surana, P. / Udgaonkar, J.B. / Das, R. / Gosavi, S.
History
DepositionApr 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: Monellin chain B,Monellin chain A
B: Monellin chain B,Monellin chain A
C: Monellin chain B,Monellin chain A
D: Monellin chain B,Monellin chain A
E: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)54,8535
Polymers54,8535
Non-polymers00
Water0
1
A: Monellin chain B,Monellin chain A
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)21,9412
Polymers21,9412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-40 kcal/mol
Surface area10750 Å2
MethodPISA
2
C: Monellin chain B,Monellin chain A
D: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)21,9412
Polymers21,9412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-37 kcal/mol
Surface area11100 Å2
MethodPISA
3
E: Monellin chain B,Monellin chain A

E: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)21,9412
Polymers21,9412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area4800 Å2
ΔGint-38 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.743, 87.265, 87.375
Angle α, β, γ (deg.)90.00, 127.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Monellin chain B,Monellin chain A / Monellin chain II / Monellin chain I


Mass: 10970.595 Da / Num. of mol.: 5
Mutation: Deletion of C-terminal of chain B, and N-terminal of chain A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli (E. coli) / References: UniProt: P02882, UniProt: P02881
Sequence detailsCHAIN B AND CHAIN A OF THE NATIVE MONELLIN PROTEIN WERE JOINED TOGETHER BY PUTTING A GLY-PHE (GF) ...CHAIN B AND CHAIN A OF THE NATIVE MONELLIN PROTEIN WERE JOINED TOGETHER BY PUTTING A GLY-PHE (GF) LINKER TO CREATE SINGLE CHAIN MONELLIN VARIANT, MNEI. THE SEQUENCE OF MNEI HAS BEEN DEPOSITED TO NCBI WITH ACCESSION AFF58925. IN THIS STUDY, RESIDUES 50-55 (NEGFRE) OF THE MNEI WERE DELETED AND ITS STRUCTURE WAS SOLVED.

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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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 12% wt/vol PEG 8000, 50mM sodium phosphate pH 6.4 / PH range: 6.0-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2016
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.611→42.932 Å / Num. obs: 19281 / % possible obs: 97.82 % / Redundancy: 3.4 % / Biso Wilson estimate: 87.38 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.034 / Net I/σ(I): 13.84
Reflection shellResolution: 2.611→2.705 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.58 / Num. unique obs: 1951 / CC1/2: 0.547 / Rpim(I) all: 0.523 / % possible all: 97.93

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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: 2.611→42.932 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / Phase error: 40.65
RfactorNum. reflection% reflectionSelection details
Rfree0.2941 979 5.08 %Random Selection
Rwork0.2596 ---
obs0.2613 19263 97.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 107.6 Å2
Refinement stepCycle: LAST / Resolution: 2.611→42.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3695 0 0 0 3695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043789
X-RAY DIFFRACTIONf_angle_d0.9645109
X-RAY DIFFRACTIONf_dihedral_angle_d12.4211459
X-RAY DIFFRACTIONf_chiral_restr0.054520
X-RAY DIFFRACTIONf_plane_restr0.006662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6113-2.74890.49521520.43752595X-RAY DIFFRACTION98
2.7489-2.92110.4511380.40862603X-RAY DIFFRACTION98
2.9211-3.14660.41051300.37952605X-RAY DIFFRACTION98
3.1466-3.46310.37371580.34222592X-RAY DIFFRACTION98
3.4631-3.96390.32881360.30262603X-RAY DIFFRACTION98
3.9639-4.99290.27971190.23492658X-RAY DIFFRACTION98
4.9929-42.9320.22381460.19652628X-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)
16.2736-1.9771-1.02134.70871.32962.09060.30830.69230.7038-0.2872-0.4389-0.705-1.1188-1.5901-0.02370.92760.00170.18330.7182-0.01480.8389-5.1369.8652-1.5543
23.90722.443-0.7892.32020.50.260.2973-0.2477-0.23440.3382-0.23820.38210.20220.447-0.01771.3532-0.10070.00390.655-0.01870.8057-16.6599-3.25852.6873
36.12451.0647-2.30653.5004-1.05495.01820.8737-1.1062-0.63580.1819-0.28241.53490.56720.9382-0.52211.1772-0.114-0.13630.71940.10831.0234-11.7405-3.46218.8831
43.84341.8482-1.8790.4471-0.33275.1936-0.27391.36370.06690.52670.15820.14180.60640.21270.12551.03030.00740.161.0239-0.07180.6803-8.121311.8068-19.9251
52.69242.4551-1.11321.9317-0.39333.8487-0.5958-0.04330.5926-0.45560.40760.2017-0.1112-1.07350.1440.9087-0.144-0.18621.47860.27331.2072-10.701822.5792-38.8234
64.40593.08044.13365.8245-2.19362.06220.9164-0.36760.19280.7744-0.5375-1.11470.70261.51010.22790.9092-0.0866-0.22741.3270.15791.09810.194317.6605-31.9466
70.6936-0.20850.96791.39740.03135.5398-0.83890.44080.5336-0.37160.79670.56610.0058-1.07320.12460.7956-0.2088-0.15741.43570.25350.9877-10.552320.1212-41.7048
83.01981.05220.21752.6358-0.49722.86770.4558-0.5226-0.1974-0.2621-0.3195-0.35920.2712-0.1692-0.17311.2156-0.10270.08380.7259-0.00340.7942-9.80250.0333-0.7521
93.6512-1.26530.57628.0776-0.64151.35590.60090.3051-0.0539-0.4048-1.21950.0798-0.08460.0470.84531.1741-0.0270.16050.98110.02810.8197-19.15695.4146-9.7746
102.9922-0.70622.67590.2389-1.14037.1165-0.2173-0.1895-0.64540.34330.2457-0.6863-0.3880.4146-0.04950.9444-0.03610.02620.58330.0031.0544-5.4492-6.78592.3608
114.5859-0.2192-0.66244.1327-0.19712.7456-0.3749-0.211-0.23760.12970.5608-0.95050.87180.23980.20970.69920.0138-0.03961.08520.08231.2955-42.271424.755740.0276
121.58562.1661-0.95123.46910.98653.2433-0.27460.1953-0.29920.13280.1763-1.1112-0.8111-0.23040.28290.8157-0.1418-0.06611.1661-0.2960.998-40.541741.971343.8904
131.8926-2.1927-2.082.4751.30763.4725-0.3135-0.66360.25650.20280.32940.1056-0.0091-0.1922-0.03710.89040.0385-0.06771.3108-0.19811.0761-45.473333.986542.4255
144.4667-2.6316-2.14922.9715-0.91863.14350.3679-0.2638-0.2959-0.8172-0.27620.1985-1.225-0.3187-0.08750.9917-0.02350.01870.7198-0.00260.7585-33.774916.42193.8366
151.8363-0.7308-0.26894.43940.5873-0.55980.6475-0.17960.1394-0.5621-0.7799-0.2444-0.3778-0.38140.09461.1501-0.0540.07370.6899-0.08510.8857-29.91816.48662.528
162.2285-0.56927.69252.505-1.43642.10932.670.11710.3832-0.051-0.59510.20020.34860.1591-1.73470.89520.13170.06211.1583-0.03311.3144-41.674615.362310.292
172.457-0.4989-0.16132.2596-1.5592.54720.58790.23830.5103-0.4858-0.18410.1296-0.17430.0316-0.33131.19310.06110.0620.7524-0.01430.8613-31.685716.8731-5.2639
181.3805-1.0392-1.24791.1031.29945.0319-0.2712-0.26790.20480.18490.4113-0.09170.4914-0.1996-0.55420.5829-0.08010.08981.1044-0.25551.0231-36.589123.506420.4597
192.1957-0.41920.17743.10840.23955.0584-0.2241-0.75730.22260.18270.8699-0.5209-0.27510.0764-0.72650.78140.02290.04021.2921-0.25051.0528-43.19634.27140.0432
204.9951.7353-2.1031.7131.46812.4807-0.49891.32410.5924-0.07570.50380.21720.0745-0.99060.01170.6851-0.00740.031.1899-0.02091.0496-48.883537.814239.4378
218.50510.4671.38018.14393.90482.0535-0.5843-0.2801-0.09160.46441.07891.4029-0.67111.0358-0.99440.99410.1420.16761.02220.05861.2211-45.84155.44229.7904
221.2383-0.03770.34021.6714-1.36360.57220.4889-0.2072-0.4117-0.2454-0.0559-0.1280.18340.0207-0.40541.30360.10530.06121.47830.20311.2847-34.0782-7.378420.6939
238.0112-1.61032.17457.1437-2.06854.9515-1.3298-0.6464-0.72940.95571.15530.0609-1.4111-0.587-0.24971.02180.01950.09651.18820.07840.8606-37.00144.966719.5887
242.21622.2774-0.78362.7362.54853.84690.0713-0.0601-0.0255-0.2702-0.33090.21681.0546-1.2070.39731.085-0.0796-0.06261.2744-0.21260.9818-65.3779-3.8598-10.2927
252.7368-1.2781-0.28574.7149-1.77611.681-0.4586-0.05420.1738-0.3149-0.7637-0.08581.0862-2.60591.22681.2052-0.3376-0.10191.775-0.38621.3123-79.6837-0.2541-12.6441
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 30:42)
4X-RAY DIFFRACTION4(chain A and resid 43:56)
5X-RAY DIFFRACTION5(chain A and resid 57:91)
6X-RAY DIFFRACTION6(chain B and resid 3:8)
7X-RAY DIFFRACTION7(chain B and resid 9:48)
8X-RAY DIFFRACTION8(chain B and resid 49:73)
9X-RAY DIFFRACTION9(chain B and resid 74:80)
10X-RAY DIFFRACTION10(chain B and resid 81:91)
11X-RAY DIFFRACTION11(chain C and resid 2:14)
12X-RAY DIFFRACTION12(chain C and resid 15:28)
13X-RAY DIFFRACTION13(chain C and resid 29:48)
14X-RAY DIFFRACTION14(chain C and resid 49:63)
15X-RAY DIFFRACTION15(chain C and resid 64:91)
16X-RAY DIFFRACTION16(chain D and resid 3:8)
17X-RAY DIFFRACTION17(chain D and resid 9:42)
18X-RAY DIFFRACTION18(chain D and resid 43:54)
19X-RAY DIFFRACTION19(chain D and resid 55:78)
20X-RAY DIFFRACTION20(chain D and resid 79:91)
21X-RAY DIFFRACTION21(chain E and resid 2:8)
22X-RAY DIFFRACTION22(chain E and resid 9:35)
23X-RAY DIFFRACTION23(chain E and resid 36:43)
24X-RAY DIFFRACTION24(chain E and resid 44:80)
25X-RAY DIFFRACTION25(chain E and resid 81:91)

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