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- PDB-4c1y: Crystal Structure of Fucose binding lectin from Aspergillus Fumig... -

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Basic information

Entry
Database: PDB / ID: 4c1y
TitleCrystal Structure of Fucose binding lectin from Aspergillus Fumigatus (AFL) in complex with b-methylfucoside
Components(FUCOSE-SPECIFIC LECTIN ...) x 2
KeywordsSUGAR BINDING PROTEIN / FUCOSIDE
Function / homology
Function and homology information


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
methyl beta-L-fucopyranoside / DI(HYDROXYETHYL)ETHER / Fucose-specific lectin
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsHouser, J. / Komarek, J. / Kostlanova, N. / Lahmann, M. / Cioci, G. / Varrot, A. / Imberty, A. / Wimmerova, M.
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
DepositionAug 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 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

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)141,05427
Polymers137,9414
Non-polymers3,11323
Water2,450136
1
A: FUCOSE-SPECIFIC LECTIN FLEA
B: FUCOSE-SPECIFIC LECTIN FLEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,93118
Polymers68,9792
Non-polymers1,95216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-15.4 kcal/mol
Surface area27900 Å2
MethodPQS
2
C: FUCOSE-SPECIFIC LECTIN FLEA
D: FUCOSE-SPECIFIC LECTIN FLEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1249
Polymers68,9632
Non-polymers1,1617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-17.3 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.211, 90.335, 189.168
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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FUCOSE-SPECIFIC LECTIN ... , 2 types, 4 molecules ABCD

#1: Protein FUCOSE-SPECIFIC LECTIN FLEA


Mass: 34497.270 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) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q4WW81
#2: Protein FUCOSE-SPECIFIC LECTIN FLEA


Mass: 34481.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q4WW81

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Sugars , 1 types, 12 molecules

#3: Sugar
ChemComp-MFB / methyl beta-L-fucopyranoside / BETA-L-METHYL-FUCOSE / methyl 6-deoxy-beta-L-galactopyranoside / methyl beta-L-fucoside / methyl L-fucoside / methyl fucoside / Methyl group


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-b-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-b-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 147 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.2 Å3/Da / Density % sol: 44.24 % / Description: NONE
Crystal growDetails: 0.2M CACL2, 25% PEG4K, 0.1M TRIS, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 21, 2011 / Details: MIRRORS
RadiationMonochromator: SI-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.23→47.29 Å / Num. obs: 56864 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.14
Reflection shellResolution: 2.23→2.29 Å / Rmerge(I) obs: 0.35 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AGI

4agi


Resolution: 2.23→48.14 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.835 / SU B: 9.545 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.31339 2993 5 %RANDOM
Rwork0.24255 ---
obs0.24611 56864 99.01 %-
Displacement parametersBiso mean: 26.964 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---1.9 Å20 Å2
3---2.63 Å2
Refinement stepCycle: LAST / Resolution: 2.23→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9754 0 203 136 10093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0210230
X-RAY DIFFRACTIONr_bond_other_d0.0020.029252
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.93713944
X-RAY DIFFRACTIONr_angle_other_deg0.791321205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.30851252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0423.702470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.163151445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2721554
X-RAY DIFFRACTIONr_chiral_restr0.0850.21501
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022556
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_it1.682.6725020
X-RAY DIFFRACTIONr_mcbond_other1.682.6725019
X-RAY DIFFRACTIONr_mcangle_it2.6824.0026268
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5412.8335210
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: 2.229→2.286 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 215 -
Rwork0.351 4095 -
obs--97.82 %

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