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- PDB-2bt9: Lectin from Ralstonia solanacearum complexed with Me-fucoside -

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Basic information

Entry
Database: PDB / ID: 2bt9
TitleLectin from Ralstonia solanacearum complexed with Me-fucoside
ComponentsLECTIN
KeywordsLECTIN / SUGAR RECOGNITION / BETA-PROPELLER
Function / homologyLipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta / methyl alpha-L-fucopyranoside / Fucose-binding lectin protein
Function and homology information
Biological speciesRALSTONIA SOLANACEARUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.94 Å
AuthorsMitchell, E.P. / Kostlanova, N. / Wimmerova, M. / Imberty, A.
CitationJournal: J. Biol. Chem. / Year: 2005
Title: The fucose-binding lectin from Ralstonia solanacearum. A new type of beta-propeller architecture formed by oligomerization and interacting with fucoside, fucosyllactose, and plant xyloglucan.
Authors: Kostlanova, N. / Mitchell, E.P. / Lortat-Jacob, H. / Oscarson, S. / Lahmann, M. / Gilboa-Garber, N. / Chambat, G. / Wimmerova, M. / Imberty, A.
History
DepositionMay 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LECTIN
B: LECTIN
C: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3189
Polymers29,2493
Non-polymers1,0696
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.985, 43.985, 103.076
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein LECTIN / HYPOTHETICAL PROTEIN RSC2107


Mass: 9749.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RALSTONIA SOLANACEARUM (bacteria) / Plasmid: PET25 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8XXK6
#2: 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.: 6
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST METHIONINE NOT IN THE MATURE PROTEIN. THE CONFLICTS IN THE SEQADV RECORDS SHOWN BELOW ARISE ...FIRST METHIONINE NOT IN THE MATURE PROTEIN. THE CONFLICTS IN THE SEQADV RECORDS SHOWN BELOW ARISE BECAUSE THIS PROTEIN IS FROM A DIFFERENT STRAIN OF RALSTONIA SOLANACEARUM.

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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: 1.7 Å3/Da / Density % sol: 25.7 %
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROPS WITH 2.5 UL RSL AT 15MG/ML, 2 UL OF RESERVOIR SOLUTION (30% PEG 6000, 0.1M TRIS/HCL PH 8.2) AND 1 UL OF GLYCINE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 31, 2005 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 0.94→30.67 Å / Num. obs: 142705 / % possible obs: 98.3 % / Redundancy: 5.79 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.32
Reflection shellResolution: 0.94→0.96 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.28 / % possible all: 79.5

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 0.94→40 Å / Num. parameters: 24240 / Num. restraintsaints: 29147 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. OCCUPANCIES OF SIDE CHAINS MODELLED IN ALTERNATIVE POSITIONS WERE ESTIMATED USING RELATIVE B-FACTORS. OCCUPANCY OF THE S-ME GROUP OF ...Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. OCCUPANCIES OF SIDE CHAINS MODELLED IN ALTERNATIVE POSITIONS WERE ESTIMATED USING RELATIVE B-FACTORS. OCCUPANCY OF THE S-ME GROUP OF METHIONINE RESIDUES WAS ESTIMATED USING DIFFERENCE MAP RESIDUALS. THESE RESIDUES HAD CLEARLY SUFFERED RADIATION DAMAGE AND HAD NO ALTERNATIVE CONFIGURATION. TOTAL NUMBER OF BINS
RfactorNum. reflection% reflectionSelection details
Rfree0.1201 7126 5 %RANDOM
all0.0976 135348 --
obs--93.5 %-
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 1876.5 / Occupancy sum non hydrogen: 2573.9
Refinement stepCycle: LAST / Resolution: 0.94→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 72 541 2648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0333
X-RAY DIFFRACTIONs_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.124
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.121

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