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- PDB-7p2i: Dimethylated fusion protein of RSL and nucleoporin peptide (Nup) ... -

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Basic information

Entry
Database: PDB / ID: 7p2i
TitleDimethylated fusion protein of RSL and nucleoporin peptide (Nup) in complex with cucurbit[7]uril, F432 cage assembly
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / biomaterials / coiled coil / crystal engineering / IDP / macrocycle
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / methyl alpha-L-fucopyranoside / cucurbit[7]uril / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.489 Å
AuthorsGuagnini, F. / Ramberg, K. / Crowley, P.B.
Funding support Ireland, 3items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation IrelandSSPC-PharM5 12/RC/2275_P2 Ireland
Irish Research CouncilGOIPD/2019/513 Ireland
CitationJournal: Chemistry / Year: 2021
Title: Segregated Protein-Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons.
Authors: Ramberg, K.O. / Guagnini, F. / Engilberge, S. / Wronska, M.A. / Rennie, M.L. / Perez, J. / Crowley, P.B.
History
DepositionJul 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,61811
Polymers33,2233
Non-polymers3,3958
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-1 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.713, 200.713, 200.713
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

21A-357-

HOH

31B-203-

HOH

41B-232-

HOH

51B-334-

HOH

61B-341-

HOH

71C-308-

HOH

81C-354-

HOH

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Components

#1: Protein Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 11074.176 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, HXP36_18875, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1
#2: Sugar
ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-QQ7 / cucurbit[7]uril


Mass: 1162.962 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H42N28O14 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25 % PEG 3350 0.1 M Bis-Tris pH 5.5 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.489→100.36 Å / Num. obs: 56936 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 25 Å2 / CC1/2: 1 / Rpim(I) all: 1.4 / Rrim(I) all: 0.012 / Net I/σ(I): 28.7
Reflection shellResolution: 1.489→1.52 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2792 / CC1/2: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (23-SEP-2019)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9


Resolution: 1.489→100.36 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.059
RfactorNum. reflection% reflectionSelection details
Rfree0.1779 2931 5.15 %RANDOM
Rwork0.1616 ---
obs0.1624 56900 100 %-
Displacement parametersBiso max: 136.73 Å2 / Biso mean: 24.94 Å2 / Biso min: 13.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: final / Resolution: 1.489→100.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 1163 473 3723
Biso mean--23.14 38.12 -
Num. residues----147
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d844SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes478HARMONIC5
X-RAY DIFFRACTIONt_it2444HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion324SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2259SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2444HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg3443HARMONIC20.77
X-RAY DIFFRACTIONt_omega_torsion5.1
X-RAY DIFFRACTIONt_other_torsion12.44
LS refinement shellResolution: 1.489→1.52 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.1979 50 4.39 %
Rwork0.1979 1088 -
obs--100 %
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)
11.2305-0.07990.13080.82620.16451.0543-0.02820.15320.0015-0.00130.0197-0.0322-0.00710.11420.0085-0.0141-0.00520.0027-0.02140.0017-0.029825.535623.608743.3178
21.5-0.18730.24160.78880.37451.2333-0.0314-0.10180.04320.11250.02340.02480.0465-0.0590.0081-0.01980.0034-0.0052-0.0581-0.0077-0.045618.185929.047860.6052
31.3655-0.1459-0.02320.87770.50521.11270.0194-0.003-0.0919-0.001-0.07980.1490.0598-0.11650.0604-0.0463-0.01590.0045-0.0512-0.0007-0.00854.717921.615846.4331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 24
2X-RAY DIFFRACTION2{ B|* }B1 - 24
3X-RAY DIFFRACTION3{ C|* }C1 - 24

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