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- PDB-4d52: CRYSTAL STRUCTURE OF FUCOSE BINDING LECTIN FROM ASPERGILLUS FUMIG... -

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Entry
Database: PDB / ID: 4d52
TitleCRYSTAL STRUCTURE OF FUCOSE BINDING LECTIN FROM ASPERGILLUS FUMIGATUS (AFL) IN COMPLEX WITH L-GALACTOPYRANOSE.
Components(FUCOSE-SPECIFIC LECTIN ...) x 3
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


adhesion of symbiont to host cell surface via host glycoprotein / carbohydrate binding / metal ion binding
Similarity search - Function
Fucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
beta-L-galactopyranose / alpha-L-galactopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Fucose-specific lectin
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHouser, J. / Cioci, G. / Komarek, J. / Wimmerowa, M. / Kostlanova, N. / Lahmann, M. / Varrot, A. / Imberty, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural Insights Into Aspergillus Fumigatus Lectin Specificity: Afl Binding Sites are Functionally Non-Equivalent.
Authors: Houser, J. / Komarek, J. / Cioci, G. / Varrot, A. / Imberty, A. / Wimmerova, M.
History
DepositionNov 1, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionMar 11, 2015ID: 4UQ7
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Jul 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_nonpoly_scheme / 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_nonpoly_scheme.ndb_seq_num / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUCOSE-SPECIFIC LECTIN FLEA
B: FUCOSE-SPECIFIC LECTIN FLEA
C: FUCOSE-SPECIFIC LECTIN FLEA
D: FUCOSE-SPECIFIC LECTIN FLEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,56149
Polymers138,5784
Non-polymers6,98345
Water19,0961060
1
A: FUCOSE-SPECIFIC LECTIN FLEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,28011
Polymers34,6121
Non-polymers1,66810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FUCOSE-SPECIFIC LECTIN FLEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,37013
Polymers34,6441
Non-polymers1,72612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FUCOSE-SPECIFIC LECTIN FLEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,71114
Polymers34,6761
Non-polymers2,03513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FUCOSE-SPECIFIC LECTIN FLEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,19911
Polymers34,6441
Non-polymers1,55410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.030, 70.440, 117.800
Angle α, β, γ (deg.)90.00, 108.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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FUCOSE-SPECIFIC LECTIN ... , 3 types, 4 molecules ABDC

#1: Protein FUCOSE-SPECIFIC LECTIN FLEA / AFL


Mass: 34612.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q4WW81
#2: Protein FUCOSE-SPECIFIC LECTIN FLEA / AFL


Mass: 34644.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q4WW81
#3: Protein FUCOSE-SPECIFIC LECTIN FLEA / AFL


Mass: 34676.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q4WW81

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Sugars , 2 types, 26 molecules

#4: Sugar
ChemComp-GXL / alpha-L-galactopyranose / alpha-L-galactose / L-galactose / galactose


Type: L-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
LGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-galactopyranoseCOMMON NAMEGMML 1.0
a-L-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar
ChemComp-GIV / beta-L-galactopyranose / beta-L-galactose / L-galactose / galactose


Type: L-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
LGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-galactopyranoseCOMMON NAMEGMML 1.0
b-L-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 1079 molecules

#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1060 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 43.8 % / Description: NONE
Crystal growDetails: 200 MM CACL2, 25% PEG 4K AND 100 MM TRIS, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→34.44 Å / Num. obs: 121067 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.2 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AGI

4agi


Resolution: 1.76→111.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.106 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 6078 5 %RANDOM
Rwork0.15374 ---
obs0.15493 114970 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20.81 Å2
2---1.41 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.76→111.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9753 0 454 1060 11267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0210406
X-RAY DIFFRACTIONr_bond_other_d0.0020.029369
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.95214178
X-RAY DIFFRACTIONr_angle_other_deg0.779321510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53651263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94623.713474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.926151448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.231555
X-RAY DIFFRACTIONr_chiral_restr0.0880.21517
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022568
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0131.6025031
X-RAY DIFFRACTIONr_mcbond_other1.0131.6025030
X-RAY DIFFRACTIONr_mcangle_it1.6192.3986286
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4421.7785375
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: 1.755→1.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 436 -
Rwork0.256 8319 -
obs--95.45 %

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