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- PDB-6su0: Crystal structure of dimethylated RSLex in complex with cucurbit[... -

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Basic information

Entry
Database: PDB / ID: 6su0
TitleCrystal structure of dimethylated RSLex in complex with cucurbit[7]uril
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / cucurbituril / molecular glue / crystal engineering
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Lipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
methyl alpha-L-fucopyranoside / cucurbit[7]uril / Fucose-binding lectin protein / Fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsGuagnini, F. / Engilberge, S. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland Ireland
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Engineered assembly of a protein-cucurbituril biohybrid.
Authors: Guagnini, F. / Engilberge, S. / Ramberg, K.O. / Perez, J. / Crowley, P.B.
History
DepositionSep 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Fucose-binding lectin protein
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
D: Fucose-binding lectin protein
E: Fucose-binding lectin protein
F: Fucose-binding lectin protein
I: Fucose-binding lectin protein
J: Fucose-binding lectin protein
K: Fucose-binding lectin protein
M: Fucose-binding lectin protein
N: Fucose-binding lectin protein
O: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,40542
Polymers118,17412
Non-polymers16,23230
Water4,990277
1
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
I: Fucose-binding lectin protein
J: Fucose-binding lectin protein
K: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,22622
Polymers59,0876
Non-polymers8,13916
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fucose-binding lectin protein
E: Fucose-binding lectin protein
F: Fucose-binding lectin protein
I: Fucose-binding lectin protein
J: Fucose-binding lectin protein
K: Fucose-binding lectin protein
M: Fucose-binding lectin protein
N: Fucose-binding lectin protein
O: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,39027
Polymers88,6309
Non-polymers11,76018
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.638, 94.534, 149.649
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 9847.815 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: RSP795_21825, RSP799_05830, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1, UniProt: Q8XXK6*PLUS
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-QQ7 / cucurbit[7]uril


Mass: 1162.962 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C42H42N28O14 / Feature type: SUBJECT OF INVESTIGATION
#4: 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.: 12
Source method: isolated from a genetically manipulated 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 1.61 Å3/Da / Density % sol: 23.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 30 % PEG 8,000 100 mM Sodium acetate; pH 4.5 200 mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.98→149.64 Å / Num. obs: 52443 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.27 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.089 / Net I/σ(I): 6
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 2608 / CC1/2: 0.09 / Rpim(I) all: 0.358

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9


Resolution: 1.98→27.32 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.837 / SU R Cruickshank DPI: 0.469 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.393 / SU Rfree Blow DPI: 0.258 / SU Rfree Cruickshank DPI: 0.266
RfactorNum. reflection% reflectionSelection details
Rfree0.311 2583 4.93 %RANDOM
Rwork0.247 ---
obs0.25 52422 99.4 %-
Displacement parametersBiso max: 209 Å2 / Biso mean: 45.23 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-5.6341 Å20 Å20.1185 Å2
2--5.9497 Å20 Å2
3----11.5838 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 1.98→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8479 0 5293 279 14051
Biso mean--45.06 32.49 -
Num. residues----540
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3637SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2084HARMONIC5
X-RAY DIFFRACTIONt_it10677HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1212SEMIHARMONIC5
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_contact11765SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10677HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15905HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion18.07
LS refinement shellResolution: 1.98→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3539 61 5.82 %
Rwork0.2091 988 -
all0.217 1049 -
obs--97.02 %
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)
11.16920.4835-0.94052.4612-0.045-0.0020.0433-0.19510.11960.1699-0.0177-0.0118-0.0782-0.052-0.0256-0.10640.0431-0.0147-0.0492-0.0169-0.13634.469536.319619.4403
21.2925-0.03770.22461.47740.75670.40060.0138-0.114-0.09780.2023-0.0282-0.15-0.01270.01740.01440.0026-0.0332-0.00250.0070.00330.01216.895416.734519.3866
31.79320.40010.68181.73820.10870.1084-0.0231-0.1630.00550.17590.04570.16360.0093-0.0178-0.02260.0110.02570.0332-0.0544-0.0036-0.0062-11.374824.418319.4061
48.45072.7997-2.2495.69281.05551.3411-0.0281-0.2050.15970.03640.0369-0.0055-0.14390.016-0.00870.3142-0.0852-0.15780.30930.15190.313638.718234.14255.4461
52.4542-2.84322.97848.5168-1.44720.17850.0289-0.02010.04250.0326-0.05310.16450.2401-0.26980.02420.3190.01080.15680.31890.10760.314222.765146.017155.4311
61.88760.0751-1.75451.50191.573-0.00370.0668-0.1470.0466-0.17050.20330.401-0.0908-0.0464-0.27010.1979-0.0172-0.01890.1981-0.02230.121220.446226.190955.4274
71.65530.3288-0.6332.3870.17260.4472-0.0596-0.22140.13420.23680.0545-0.1731-0.0330.16290.0051-0.06590.01620.0144-0.06880.00040.170711.346927.177319.4066
81.29270.13230.60072.09740.12160.09990.0526-0.228-0.13820.1397-0.0208-0.02760.1025-0.0815-0.0318-0.10070.00320.0069-0.03280.0080.1916-4.461215.31919.3678
91.6873-0.6197-0.18221.8535-0.74830.92630.0104-0.17620.09720.3554-0.004-0.0384-0.1682-0.0674-0.0064-0.0887-0.0590.0018-0.04320.00950.2095-6.900134.997319.3461
100-0.0138-0.00930-0.0140.0025-0.01350.0034-0.0199-0.01480.00720.0299-0.01960.01830.0063-0.0660.00370.0211-0.01970.00440.152713.593130.628637.4145
113.4068-0.1661-1.06441.92041.0872-0.00220.11240.216-0.36990.0271-00.0725-0.0031-0.0258-0.11240.17790.0091-0.02240.1528-0.01110.109331.817424.872755.4281
121.9557-0.59840.76923.01490.12490.42480.10780.1048-0.0686-0.2556-0.0561-0.2762-0.0470.0241-0.05170.19010.00540.00540.2020.01030.110934.153844.573955.3979
132.7094-0.4908-0.05941.11091.40671.54440.0729-0.0789-0.23290.1306-0.0514-0.00740.1802-0.0402-0.02150.1891-0.0224-0.02240.1222-0.01460.039515.823436.708255.4974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 24
2X-RAY DIFFRACTION2{ B|* }B2 - 24
3X-RAY DIFFRACTION3{ C|* }C2 - 24
4X-RAY DIFFRACTION4{ D|* }D2 - 24
5X-RAY DIFFRACTION5{ E|* }E2 - 24
6X-RAY DIFFRACTION6{ F|* }F2 - 24
7X-RAY DIFFRACTION7{ I|* }I2 - 24
8X-RAY DIFFRACTION8{ J|* }J2 - 24
9X-RAY DIFFRACTION9{ K|* }K2 - 24
10X-RAY DIFFRACTION10{ L|* }L1 - 12
11X-RAY DIFFRACTION11{ M|* }M2 - 24
12X-RAY DIFFRACTION12{ N|* }N2 - 24
13X-RAY DIFFRACTION13{ O|* }O2 - 24

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