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- PDB-7p2j: Dimethylated fusion protein of RSL and trimeric coiled coil (4dzn... -

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Basic information

Entry
Database: PDB / ID: 7p2j
TitleDimethylated fusion protein of RSL and trimeric coiled coil (4dzn) in complex with cucurbit[7]uril, H3 sheet 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 / beta-D-mannopyranose / cucurbit[7]uril / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsRamberg, K. / Engilberge, S. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation IrelandSSPC-PharM5 12/RC/2275_P2 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: Data collection / Database references / Category: citation / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,78610
Polymers24,6942
Non-polymers3,0938
Water4,360242
1
A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,67915
Polymers37,0403
Non-polymers4,63912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8120 Å2
ΔGint-7 kcal/mol
Surface area18000 Å2
MethodPISA
2
B: Fucose-binding lectin protein
hetero molecules

B: Fucose-binding lectin protein
hetero molecules

B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,67915
Polymers37,0403
Non-polymers4,63912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8070 Å2
ΔGint-14 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.617, 51.617, 322.633
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-104-

NA

21B-104-

NA

31A-279-

HOH

41A-286-

HOH

51A-293-

HOH

61A-306-

HOH

71A-324-

HOH

81B-281-

HOH

91B-299-

HOH

101B-317-

HOH

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Components

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


Mass: 12346.774 Da / Num. of mol.: 2
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: 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
#3: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.23 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 % PEG 8000 0.1 M Tris-HCl pH 8.5 0.2 M MgCl2 2 mM Q7

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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: 1.98→107.54 Å / Num. obs: 22317 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 31.68 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.055 / Rrim(I) all: 0.17 / Net I/σ(I): 6.8
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1086 / CC1/2: 0.85 / Rpim(I) all: 0.334 / Rrim(I) all: 0.916 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9


Resolution: 1.98→107.54 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 33.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 1082 4.85 %
Rwork0.201 21213 -
obs0.2033 22295 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.79 Å2 / Biso mean: 43.125 Å2 / Biso min: 24.62 Å2
Refinement stepCycle: final / Resolution: 1.98→107.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 218 243 2127
Biso mean--39.48 44.49 -
Num. residues----204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.98-2.070.3861420.318726572799
2.07-2.180.3441370.284326102747
2.18-2.320.27361460.247826442790
2.32-2.490.29311140.221426672781
2.49-2.750.29151440.225726492793
2.75-3.140.30361290.214226542783
3.14-3.960.22051320.178626742806
3.96-43.080.18511380.160726582796

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