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- PDB-1ovp: LecB (PA-LII) in complex with fructose -

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Basic information

Entry
Database: PDB / ID: 1ovp
TitleLecB (PA-LII) in complex with fructose
Componentshypothetical protein LecBHypothesis
KeywordsSUGAR BINDING PROTEIN / lectin / carbohydrate
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-fructopyranose / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLoris, R. / Tielker, D. / Jaeger, K.-E. / Wyns, L.
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: Structural Basis of Carbohydrate Recognition by the Lectin LecB from Pseudomonas aeruginosa
Authors: Loris, R. / Tielker, D. / Jaeger, K.-E. / Wyns, L.
History
DepositionMar 27, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_label_seq_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.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_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_seq_id / _struct_conn.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 13, 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: hypothetical protein LecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9954
Polymers11,7351
Non-polymers2603
Water3,315184
1
A: hypothetical protein LecB
hetero molecules

A: hypothetical protein LecB
hetero molecules

A: hypothetical protein LecB
hetero molecules

A: hypothetical protein LecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,98016
Polymers46,9394
Non-polymers1,04112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)53.06, 69.05, 74.09
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

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Components

#1: Protein hypothetical protein LecB / Hypothesis / LecB


Mass: 11734.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: LecB / Plasmid: pET22a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYN5
#2: Sugar ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose / Fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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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: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG8000, ammonium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG80001reservoir
2150 mMammonium sulfate1reservoir
35 mg/mlprotein1drop
4100 mMTris1droppH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 21, 2002 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→15 Å / Num. all: 26791 / Num. obs: 26791 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.087 / Num. unique all: 2657 / % possible all: 99.7
Reflection
*PLUS
% possible obs: 98.8 % / Num. measured all: 155542 / Rmerge(I) obs: 0.061

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1971 2130 random
Rwork0.1821 --
all0.1833 26791 -
obs0.1833 26791 -
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 14 184 1025
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.102007
X-RAY DIFFRACTIONc_angle_d1.56138
Refinement
*PLUS
Rfactor Rfree: 0.197 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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