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- PDB-1oko: Crystal structure of Pseudomonas Aeruginosa Lectin 1 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1oko
TitleCrystal structure of Pseudomonas Aeruginosa Lectin 1 complexed with galactose at 1.6 A resolution
ComponentsPA-I GALACTOPHILIC LECTIN
KeywordsSUGAR BINDING PROTEIN / GALACTOSE BINDING
Function / homology
Function and homology information


heterophilic cell-cell adhesion / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding lectin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-galactopyranose / alpha-D-galactopyranose / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCioci, G. / Mitchell, E. / Gautier, C. / Wimmerova, M. / Perez, S. / Gilboa-Garber, N. / Imberty, A.
CitationJournal: FEBS Lett. / Year: 2003
Title: Structural Basis of Calcium and Galactose Recognition by the Lectin Pa-Il of Pseudomonas Aeruginosa
Authors: Cioci, G. / Mitchell, E. / Gautier, C. / Wimmerova, M. / Sudakevitz, D. / Perez, S. / Gilboa-Garber, N. / Imberty, A.
History
DepositionJul 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2003Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 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 / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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.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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PA-I GALACTOPHILIC LECTIN
B: PA-I GALACTOPHILIC LECTIN
C: PA-I GALACTOPHILIC LECTIN
D: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,90819
Polymers51,0814
Non-polymers1,82815
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-17.6 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.057, 53.275, 160.675
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PA-I GALACTOPHILIC LECTIN / PA-IL / GALACTOSE-BINDING LECTIN


Mass: 12770.137 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: Q05097

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Sugars , 2 types, 7 molecules

#3: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 490 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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 Å3/Da / Density % sol: 37 % / Description: RFREE MERGED FROM EBI-13164
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP: PROTEIN SOLUTION: PA1L 5 MG/ML, D-GAL 0.025 MG/ML, CACL2 & MGCL2 2MM RESERVOIR SOLUTION: (NH4)2SO4 1.5 M, PH 4.7, 5% MPD, 2% GLYCEROL 2 UL + 2 UL
Crystal grow
*PLUS
pH: 4.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.5 Mammonium sulfate1reservoirpH4.7
35 %MPD1reservoir
42 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2003 / Details: MULTILAYER
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→18.6 Å / Num. obs: 53762 / % possible obs: 94.9 % / Redundancy: 4.49 % / Biso Wilson estimate: 12.535 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 6.6701
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.23 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.42 / % possible all: 79.1
Reflection
*PLUS
Highest resolution: 1.6 Å / Redundancy: 4.5 % / Num. measured all: 241596 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 79.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MONOMER B FROM PREVIOULSY RESOLVED 1OKP

1okp


Resolution: 1.6→18.602 Å / SU B: 1.779 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 2730 5.18 %RANDOM
Rwork0.1541 ---
obs0.1557 51032 94.94 %-
Displacement parametersBiso mean: 11.301 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.9 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 111 482 4197
Refinement
*PLUS
Lowest resolution: 18.6 Å / Rfactor Rfree: 0.187 / Rfactor Rwork: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.017
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.57
LS refinement shell
*PLUS
Rfactor Rfree: 0.256 / Num. reflection Rfree: 144 / Rfactor Rwork: 0.197 / Num. reflection Rwork: 3066

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