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- PDB-1ous: Lecb (PA-LII) calcium-free -

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Basic information

Entry
Database: PDB / ID: 1ous
TitleLecb (PA-LII) calcium-free
Componentshypothetical protein LecB
KeywordsSUGAR BINDING PROTEIN / lectin / carbohydrate
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Calcium-mediated lectin / Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 25, 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein LecB
B: hypothetical protein LecB
C: hypothetical protein LecB
D: hypothetical protein LecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0355
Polymers46,9394
Non-polymers961
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-53 kcal/mol
Surface area15270 Å2
MethodPISA
2
A: hypothetical protein LecB
B: hypothetical protein LecB
hetero molecules

C: hypothetical protein LecB
D: hypothetical protein LecB


Theoretical massNumber of molelcules
Total (without water)47,0355
Polymers46,9394
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
Buried area6420 Å2
ΔGint-61 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.81, 73.80, 100.11
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
hypothetical protein LecB / LecB


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: LecB / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYN5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 1.63 Å3/Da / Density % sol: 24.04 %
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: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMEDTA1drop
230-35 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 12, 2002 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.2→17 Å / Num. all: 104894 / Num. obs: 104894 / % possible obs: 95.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.35
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.185 / % possible all: 88.3
Reflection
*PLUS
Num. obs: 104887 / Num. measured all: 356581

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→17 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.209 8464 random
Rwork0.198 --
all0.199 104887 -
obs0.199 104887 -
Refinement stepCycle: LAST / Resolution: 1.2→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 5 569 3784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005155
X-RAY DIFFRACTIONc_angle_deg1.47576
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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