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- PDB-4i6s: Structure of RSL mutant W76A in complex with L-fucose -

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Basic information

Entry
Database: PDB / ID: 4i6s
TitleStructure of RSL mutant W76A in complex with L-fucose
ComponentsPutative fucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / lectin / beta-propeller / L-fucose / multivalency / Trivalent Fucose binding lectin / Fucosylated oligosaccharides binding / Soluble
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
alpha-L-fucopyranose / beta-L-fucopyranose / Putative fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsAudfray, A. / Arnaud, J. / Varrot, A. / Imberty, A.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Reduction of lectin valency drastically changes glycolipid dynamics in membranes but not surface avidity
Authors: Arnaud, J. / Claudinon, J. / Trondle, K. / Trovaslet, M. / Larson, G. / Thomas, A. / Varrot, A. / Romer, W. / Imberty, A. / Audfray, A.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,17715
Polymers29,2493
Non-polymers1,92812
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-20 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.765, 103.765, 100.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-105-

PG4

21B-241-

HOH

31B-273-

HOH

41B-281-

HOH

51C-250-

HOH

61C-284-

HOH

71C-285-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.277246, -0.222116, -0.934772), (0.949111, 0.087979, -0.302404), (0.149409, -0.971043, 0.186421)-31.60168, 30.54858, 10.18765

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Putative fucose-binding lectin protein


Mass: 9749.626 Da / Num. of mol.: 3 / Mutation: W76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Strain: ATCC 11696 / Gene: CMR15_11270, rsc2107 / Plasmid: pET25 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: D8NA05

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Sugars , 2 types, 9 molecules

#2: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 288 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsHETEROGEN FUC(102 CHAIN A) AND FUL(103 CHAIN A) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. ...HETEROGEN FUC(102 CHAIN A) AND FUL(103 CHAIN A) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. FUC(102 CHAIN B) AND FUL(103 CHAIN B) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. FUC(101 CHAIN C) AND FUL(102 CHAIN C) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris/Bicine, 0.12M Monosaccharides, 30% P550MME/P20K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9817 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2012
Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9817 Å / Relative weight: 1
ReflectionResolution: 1.54→51.88 Å / Num. obs: 41015 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 24.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.54-1.627.70.3475.158650.34799.1
4.86-51.888.80.02954.914360.02999.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9


Resolution: 1.54→51.88 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.104 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17173 2061 5 %RANDOM
Rwork0.1481 ---
obs0.14925 38902 99.54 %-
all-41169 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.54→51.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 120 285 2412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022209
X-RAY DIFFRACTIONr_bond_other_d0.0020.021918
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9333034
X-RAY DIFFRACTIONr_angle_other_deg0.79934395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1245269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21723.49483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2215279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.951159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
LS refinement shellResolution: 1.54→1.576 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 140 -
Rwork0.193 2793 -
obs--97.8 %
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)
11.7889-0.33420.49020.62270.2190.6501-0.1762-0.26560.34310.04230.1471-0.1126-0.06090.0480.02920.04990.0365-0.02170.079-0.07470.1076-24.06552.278916.4799
21.3895-0.030.55670.70880.57991.13990.00330.06850.0177-0.0352-0.00330.0236-0.00110.0263-0.00010.03240.01060.01320.0403-0.00930.0215-27.9047-9.95662.5206
32.2326-0.66720.16360.2021-0.05180.0222-0.0695-0.06030.08010.03280.036-0.0188-0.0253-0.02810.03350.05480.0492-0.01330.0581-0.03540.0951-43.64710.04427.5904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 89
2X-RAY DIFFRACTION2B1 - 89
3X-RAY DIFFRACTION3C2 - 89

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