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- PDB-2wyf: Crystal structure of PA-IL lectin complexed with aGal12bGal-O-Met... -

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Basic information

Entry
Database: PDB / ID: 2wyf
TitleCrystal structure of PA-IL lectin complexed with aGal12bGal-O-Met at 2.4 A resolution
ComponentsPA-I GALACTOPHILIC LECTIN
KeywordsSUGAR BINDING PROTEIN / LECTIN
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-D-galactopyranose / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNurisso, A. / Blanchard, B. / Varrot, A. / Imberty, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Role of Water Molecules in Structure and Energetics of Pseudomonas Aeruginosa Lectin I Interacting with Disaccharides.
Authors: Nurisso, A. / Blanchard, B. / Audfray, A. / Rydner, L. / Oscarson, S. / Varrot, A. / Imberty, A.
History
DepositionNov 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Source and taxonomy / Version format compliance
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 / 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_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.mon_nstd_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)104,98024
Polymers102,1618
Non-polymers2,81916
Water11,638646
1
A: PA-I GALACTOPHILIC LECTIN
B: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1576
Polymers25,5402
Non-polymers6174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-22.1 kcal/mol
Surface area10700 Å2
MethodPISA
2
C: PA-I GALACTOPHILIC LECTIN
D: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3336
Polymers25,5402
Non-polymers7934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-22.2 kcal/mol
Surface area10850 Å2
MethodPISA
3
E: PA-I GALACTOPHILIC LECTIN
F: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1576
Polymers25,5402
Non-polymers6174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-24 kcal/mol
Surface area10730 Å2
MethodPISA
4
G: PA-I GALACTOPHILIC LECTIN
H: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3336
Polymers25,5402
Non-polymers7934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-19.8 kcal/mol
Surface area10730 Å2
MethodPISA
5
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)52,49012
Polymers51,0814
Non-polymers1,4098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
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)52,49012
Polymers51,0814
Non-polymers1,4098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.885, 99.788, 91.318
Angle α, β, γ (deg.)90.00, 100.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 12770.137 Da / Num. of mol.: 8 / Fragment: RESIDUES 2-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097
#2: Polysaccharide
alpha-D-galactopyranose-(1-2)-methyl beta-D-galactopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-2DGalp[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OC][a2112h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Galp]{[(2+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#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.: 2
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL METHIONINE CLEAVED

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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: 1.98 Å3/Da / Density % sol: 37.54 % / Description: NONE
Crystal growpH: 4
Details: 15% PEG 6000, 1M LITHIUM CHLORIDE, 100MM CITRIC ACID PH 4.0

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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: Mar 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→37.11 Å / Num. obs: 32401 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OKO

1oko


Resolution: 2.4→89.8 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.864 / SU B: 9.215 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 1.881 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25891 1718 5 %RANDOM
Rwork0.16574 ---
obs0.1704 32401 99.06 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.294 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.24 Å2
2--0.69 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→89.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7185 0 176 646 8007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227541
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.94310320
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5625957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49525.841327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.582151031
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.081516
X-RAY DIFFRACTIONr_chiral_restr0.1060.21156
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025796
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.23345
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.24942
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2547
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1040.218
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7251.54861
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17227594
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.65933146
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5244.52726
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 150 -
Rwork0.208 2401 -
obs--99.73 %

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