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- PDB-4al9: Crystal structure of the lectin PA-IL from Pseudomonas aeruginoas... -

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Basic information

Entry
Database: PDB / ID: 4al9
TitleCrystal structure of the lectin PA-IL from Pseudomonas aeruginoas in complex with melibiose
ComponentsPA-I GALACTOPHILIC LECTIN
KeywordsSUGAR BINDING PROTEIN / GALACTOSE BINDING PROTEIN
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / 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
alpha-melibiose / alpha-D-galactopyranose / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBlanchard, B. / Imberty, A. / Varrot, A.
CitationJournal: Proteins / Year: 2014
Title: Secondary Sugar Binding Site Identified for Leca Lectin from Pseudomonas Aeruginosa.
Authors: Blanchard, B. / Imberty, A. / Varrot, A.
History
DepositionMar 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Sep 16, 2015Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: 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 650 HELIX 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
E: PA-I GALACTOPHILIC LECTIN
F: PA-I GALACTOPHILIC LECTIN
G: PA-I GALACTOPHILIC LECTIN
H: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,55829
Polymers102,1618
Non-polymers2,39621
Water13,601755
1
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)52,08614
Polymers51,0814
Non-polymers1,00510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: PA-I GALACTOPHILIC LECTIN
F: PA-I GALACTOPHILIC LECTIN
G: PA-I GALACTOPHILIC LECTIN
H: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,47215
Polymers51,0814
Non-polymers1,39111
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.070, 58.130, 75.940
Angle α, β, γ (deg.)101.13, 92.89, 100.98
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9865, -0.0824, -0.1414), (-0.0568, -0.638, 0.7679), (-0.1535, 0.7656, 0.6247)-40.63, -52.36, 21.23
2given(-0.9341, -0.3164, 0.1653), (-0.3172, 0.5234, -0.7908), (0.1637, -0.7912, -0.5893)-45.79, -28.48, -35.73
3given(0.9149, 0.4035, -0.0136), (0.4035, -0.9132, 0.0567), (0.0104, -0.0574, -0.9983)12.27, -58.61, -16.02
4given(-0.9799, 0.1022, 0.1712), (0.08604, -0.558, 0.8254), (0.1799, 0.8235, 0.538)-7.316, 0.6541, 0.5206
5given(-0.9223, 0.3375, -0.1882), (0.3513, 0.53, -0.7718), (-0.1607, -0.778, -0.6074)-9.065, -8.392, -18.78
6given(0.9058, -0.4237, 0.0016), (-0.4221, -0.9026, -0.0846), (0.0372, 0.0759, -0.9964)-2.679, -11.88, -18.52

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 12770.137 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: N TERMINAL METHIONINE PROCESSED / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097

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Sugars , 2 types, 8 molecules

#2: Polysaccharide alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose / alpha-melibiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-melibiose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Galp]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6
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 , 3 types, 768 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.09 Å3/Da / Density % sol: 41.05 % / Description: NONE
Crystal growpH: 4.6
Details: 15% PEG5KMME, 100 MM SODIUM ACETATE PH 4.6, 100MM KSCN, 20% GLYCEROL (ADDED FOR CRYPROTECTION)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH QUANTUM 4 / Detector: CCD / Date: Jun 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.75→30.95 Å / Num. obs: 76423 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4 / % possible all: 65.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OKO

1oko


Resolution: 1.75→30.95 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.542 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21134 3824 5 %RANDOM
Rwork0.16659 ---
obs0.16881 72599 92.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.251 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.49 Å2-0.19 Å2
2--0.06 Å2-1.16 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7208 0 146 755 8109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.027627
X-RAY DIFFRACTIONr_bond_other_d0.0010.024855
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.93910451
X-RAY DIFFRACTIONr_angle_other_deg0.872311939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92325.891331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.2061516
X-RAY DIFFRACTIONr_chiral_restr0.0960.21156
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021462
X-RAY DIFFRACTIONr_nbd_refined0.2442064
X-RAY DIFFRACTIONr_nbd_other0.24913
X-RAY DIFFRACTIONr_nbtor_refined0.180.23849
X-RAY DIFFRACTIONr_nbtor_other0.23749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1040.230
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.265
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 175 -
Rwork0.23 3440 -
obs--58.77 %

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