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- PDB-6t9a: Crystal structrue of RSL W31FW76F lectin mutant in complex with L... -

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Basic information

Entry
Database: PDB / ID: 6t9a
TitleCrystal structrue of RSL W31FW76F lectin mutant in complex with L-fucose
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / lectin / beta-propeller / fucose-binding
Function / homology
Function and homology information


carbohydrate 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 / Fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHouser, J. / Kozmon, S. / Wimmerova, M.
CitationJournal: Chemistry / Year: 2020
Title: The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification.
Authors: Houser, J. / Kozmon, S. / Mishra, D. / Hammerova, Z. / Wimmerova, M. / Koca, J.
History
DepositionOct 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 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 / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 12, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,95817
Polymers28,9663
Non-polymers1,99214
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint27 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.262, 42.105, 44.020
Angle α, β, γ (deg.)116.400, 94.540, 115.490
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 9655.491 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Double mutant W31F W76F / 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
#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 / Feature type: SUBJECT OF INVESTIGATION
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.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 1.9 Å3/Da / Density % sol: 35.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 23% PEG 6000, 0.1M Glycine, 0.1M Tris/HCl, pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→37.15 Å / Num. all: 14315 / Num. obs: 14315 / % possible obs: 96.4 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.048 / Rrim(I) all: 0.071 / Rsym value: 0.053 / Net I/σ(I): 8.3 / Num. measured all: 28355
Reflection shellResolution: 2→2.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.16 / Num. unique obs: 2071 / CC1/2: 0.933 / Rpim(I) all: 0.041 / Rrim(I) all: 0.063 / Rsym value: 0.047 / % possible all: 95.3

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9


Resolution: 2→37.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.324 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.171
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 789 5.5 %RANDOM
Rwork0.1522 ---
obs0.1547 13517 96.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 57.58 Å2 / Biso mean: 23.392 Å2 / Biso min: 15.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-1.32 Å2-0.94 Å2
2--0.64 Å20.83 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 2→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 133 255 2365
Biso mean--23.13 34.44 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132170
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181834
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.732982
X-RAY DIFFRACTIONr_angle_other_deg1.1371.6544237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4595262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80121.75891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.37515262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.174159
X-RAY DIFFRACTIONr_chiral_restr0.0380.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02489
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 53 -
Rwork0.193 944 -
all-997 -
obs--95.13 %

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