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- PDB-6zul: Crystal structure of dimethylated RSL in complex with cucurbit[7]... -

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Basic information

Entry
Database: PDB / ID: 6zul
TitleCrystal structure of dimethylated RSL in complex with cucurbit[7]uril and zinc
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / cucurbituril / molecular glue / crystal engineering / dimethyllysine / zinc / b-propeller
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / cucurbit[7]uril / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsGuagnini, F. / Engilberge, S. / Flood, R.J. / Ramberg, K.O. / Crowley, P.B.
Funding support Ireland, 3items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation Ireland12/RC/2275_P2 Ireland
Irish Research CouncilGOIPD/2019/513 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2020
Title: Metal-Mediated Protein-Cucurbituril Crystalline Architectures
Authors: Guagnini, F. / Engilberge, S. / Flood, R.J. / Ramberg, K.O. / Crowley, P.B.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,36230
Polymers59,0576
Non-polymers8,30624
Water10,701594
1
A: Fucose-binding lectin protein
C: Fucose-binding lectin protein
E: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,74716
Polymers29,5283
Non-polymers4,21813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-44 kcal/mol
Surface area13180 Å2
MethodPISA
2
B: Fucose-binding lectin protein
D: Fucose-binding lectin protein
F: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,61614
Polymers29,5283
Non-polymers4,08711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-45 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.358, 50.356, 71.513
Angle α, β, γ (deg.)84.170, 82.460, 60.040
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 89)
21(chain B and (resid 2 through 82 or (resid 83...
31(chain C and (resid 2 through 82 or (resid 83...
41(chain D and (resid 2 through 82 or (resid 83...
51(chain E and (resid 2 through 82 or (resid 83...
61(chain F and (resid 2 through 82 or (resid 83...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 2 through 89)A2 - 89
211(chain B and (resid 2 through 82 or (resid 83...B2 - 82
221(chain B and (resid 2 through 82 or (resid 83...B83
231(chain B and (resid 2 through 82 or (resid 83...B1 - 301
241(chain B and (resid 2 through 82 or (resid 83...B1 - 301
251(chain B and (resid 2 through 82 or (resid 83...B1 - 301
261(chain B and (resid 2 through 82 or (resid 83...B1 - 301
271(chain B and (resid 2 through 82 or (resid 83...B1 - 301
281(chain B and (resid 2 through 82 or (resid 83...B1 - 301
291(chain B and (resid 2 through 82 or (resid 83...B1 - 301
2101(chain B and (resid 2 through 82 or (resid 83...B1 - 301
2111(chain B and (resid 2 through 82 or (resid 83...B1 - 301
311(chain C and (resid 2 through 82 or (resid 83...C2 - 82
321(chain C and (resid 2 through 82 or (resid 83...C83
331(chain C and (resid 2 through 82 or (resid 83...C1 - 301
341(chain C and (resid 2 through 82 or (resid 83...C1 - 301
351(chain C and (resid 2 through 82 or (resid 83...C1 - 301
361(chain C and (resid 2 through 82 or (resid 83...C1 - 301
371(chain C and (resid 2 through 82 or (resid 83...C1 - 301
381(chain C and (resid 2 through 82 or (resid 83...C1 - 301
391(chain C and (resid 2 through 82 or (resid 83...C1 - 301
3101(chain C and (resid 2 through 82 or (resid 83...C1 - 301
411(chain D and (resid 2 through 82 or (resid 83...D2 - 82
421(chain D and (resid 2 through 82 or (resid 83...D83
431(chain D and (resid 2 through 82 or (resid 83...D1 - 401
441(chain D and (resid 2 through 82 or (resid 83...D1 - 401
451(chain D and (resid 2 through 82 or (resid 83...D1 - 401
461(chain D and (resid 2 through 82 or (resid 83...D1 - 401
471(chain D and (resid 2 through 82 or (resid 83...D1 - 401
481(chain D and (resid 2 through 82 or (resid 83...D1 - 401
491(chain D and (resid 2 through 82 or (resid 83...D1 - 401
4101(chain D and (resid 2 through 82 or (resid 83...D1 - 401
4111(chain D and (resid 2 through 82 or (resid 83...D1 - 401
511(chain E and (resid 2 through 82 or (resid 83...E2 - 82
521(chain E and (resid 2 through 82 or (resid 83...E83
531(chain E and (resid 2 through 82 or (resid 83...E1 - 301
541(chain E and (resid 2 through 82 or (resid 83...E1 - 301
551(chain E and (resid 2 through 82 or (resid 83...E1 - 301
561(chain E and (resid 2 through 82 or (resid 83...E1 - 301
571(chain E and (resid 2 through 82 or (resid 83...E1 - 301
581(chain E and (resid 2 through 82 or (resid 83...E1 - 301
591(chain E and (resid 2 through 82 or (resid 83...E1 - 301
5101(chain E and (resid 2 through 82 or (resid 83...E1 - 301
5111(chain E and (resid 2 through 82 or (resid 83...E1 - 301
611(chain F and (resid 2 through 82 or (resid 83...F2 - 82
621(chain F and (resid 2 through 82 or (resid 83...F83
631(chain F and (resid 2 through 82 or (resid 83...F1 - 301
641(chain F and (resid 2 through 82 or (resid 83...F1 - 301
651(chain F and (resid 2 through 82 or (resid 83...F1 - 301
661(chain F and (resid 2 through 82 or (resid 83...F1 - 301
671(chain F and (resid 2 through 82 or (resid 83...F1 - 301
681(chain F and (resid 2 through 82 or (resid 83...F1 - 301
691(chain F and (resid 2 through 82 or (resid 83...F1 - 301
6101(chain F and (resid 2 through 82 or (resid 83...F1 - 301
6111(chain F and (resid 2 through 82 or (resid 83...F1 - 301

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 9842.753 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1

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Non-polymers , 5 types, 618 molecules

#2: Chemical
ChemComp-QQ7 / cucurbit[7]uril


Mass: 1162.962 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H42N28O14 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.86 % / Description: hexagonal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 8000, 0.1 M BIS-TRIS pH 7.0

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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 EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.617→43.437 Å / Num. obs: 73881 / % possible obs: 95.9 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.051 / Rrim(I) all: 0.096 / Net I/σ(I): 5.7
Reflection shellResolution: 1.617→1.645 Å / Rmerge(I) obs: 0.406 / Num. unique obs: 3534 / CC1/2: 0.906 / Rpim(I) all: 0.271 / Rrim(I) all: 0.491

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F7W polyalanine

6f7w


Resolution: 1.62→43.437 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 3696 5 %
Rwork0.1741 70170 -
obs0.1758 73866 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.16 Å2 / Biso mean: 15.6035 Å2 / Biso min: 2.61 Å2
Refinement stepCycle: final / Resolution: 1.62→43.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 930 599 5690
Biso mean--15.87 27.44 -
Num. residues----539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074976
X-RAY DIFFRACTIONf_angle_d0.9257046
X-RAY DIFFRACTIONf_chiral_restr0.057640
X-RAY DIFFRACTIONf_plane_restr0.0151059
X-RAY DIFFRACTIONf_dihedral_angle_d9.7292877
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2264X-RAY DIFFRACTION11.403TORSIONAL
12B2264X-RAY DIFFRACTION11.403TORSIONAL
13C2264X-RAY DIFFRACTION11.403TORSIONAL
14D2264X-RAY DIFFRACTION11.403TORSIONAL
15E2264X-RAY DIFFRACTION11.403TORSIONAL
16F2264X-RAY DIFFRACTION11.403TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.62-1.63830.45081300.3552259793
1.6383-1.66070.37131620.335258093
1.6607-1.68450.35451480.2882263893
1.6845-1.70960.30531480.2846262594
1.7096-1.73630.36321490.2949265393
1.7363-1.76480.32971630.2988254494
1.7648-1.79520.28161600.2412268094
1.7952-1.82790.22091380.1863261994
1.8279-1.8630.22791480.1702273496
1.863-1.9010.20121420.1569265696
1.901-1.94240.21511240.1599277496
1.9424-1.98760.20271320.1619270396
1.9876-2.03730.19861340.1559271497
2.0373-2.09230.20151650.1636272797
2.0923-2.15390.21531590.1691268397
2.1539-2.22340.20141510.1676271496
2.2234-2.30290.19361370.1634275696
2.3029-2.39510.19451070.1674278398
2.3951-2.50410.18731090.1632277197
2.5041-2.63610.21691370.1744273698
2.6361-2.80120.20561620.1622273197
2.8012-3.01750.2131530.164268597
3.0175-3.3210.16651580.1431272197
3.321-3.80130.19961140.1502280798
3.8013-4.78830.14271690.1399274799
4.7883-43.4370.1794970.1653279297
Refinement TLS params.Method: refined / Origin x: -7.3195 Å / Origin y: 18.0442 Å / Origin z: 14.5615 Å
111213212223313233
T0.0272 Å2-0.0018 Å20.0016 Å2-0.0309 Å20.0009 Å2--0.0329 Å2
L0.0633 °2-0.0148 °2-0.0025 °2-0.093 °20.0258 °2--0.0434 °2
S0.0118 Å °-0.0099 Å °-0.0062 Å °0.0086 Å °0.02 Å °0.0037 Å °0.0006 Å °0.0034 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 401
2X-RAY DIFFRACTION1allB1 - 301
3X-RAY DIFFRACTION1allC1 - 301
4X-RAY DIFFRACTION1allD1 - 401
5X-RAY DIFFRACTION1allE1 - 301
6X-RAY DIFFRACTION1allF1 - 301
7X-RAY DIFFRACTION1allG1 - 2
8X-RAY DIFFRACTION1allH1 - 3
9X-RAY DIFFRACTION1allW1 - 621

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