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- PDB-6gke: Aleuria aurantia lectin AAL N224Q mutant in complex with Fucalpha... -

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Basic information

Entry
Database: PDB / ID: 6gke
TitleAleuria aurantia lectin AAL N224Q mutant in complex with Fucalpha1-6GlcNAc
ComponentsFucose-specific lectin
KeywordsSUGAR BINDING PROTEIN / lectin / propeller / fucose
Function / homology
Function and homology information


reproductive fruiting body development / fucose binding / defense response to fungus / carbohydrate binding / protein homodimerization activity / identical protein binding
Similarity search - Function
Fucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / Fucose-specific lectin
Similarity search - Component
Biological speciesAleuria aurantia (orange peel mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsHouser, J. / Wimmerova, M. / Herrera, H. / Mehta, A.S.
CitationJournal: To Be Published
Title: Structural dynamics and applications of a fucose-binding lectin with enhanced binding to alpha-1,6-linked core fucosylation
Authors: Herrera, H. / Wang, M. / Romano, P. / Wimmerova, M. / Houser, J. / Kortagere, S. / Mehta, A.S.
History
DepositionMay 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,51811
Polymers35,0641
Non-polymers1,45410
Water8,791488
1
A: Fucose-specific lectin
hetero molecules

A: Fucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,03622
Polymers70,1272
Non-polymers2,90920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6300 Å2
ΔGint13 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.320, 48.650, 57.610
Angle α, β, γ (deg.)90.00, 103.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fucose-specific lectin / Aleuria aurantia lectin / AAL


Mass: 35063.730 Da / Num. of mol.: 1 / Mutation: N224Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aleuria aurantia (orange peel mushroom)
Plasmid: pD444-ompA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: P18891

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Sugars , 2 types, 5 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 493 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 12% PEG6000, 0.12 M citrate buffer pH 5.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.08→17.61 Å / Num. obs: 151349 / % possible obs: 99.2 % / Redundancy: 4 % / Biso Wilson estimate: 5.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.035 / Rrim(I) all: 0.072 / Net I/σ(I): 12.1
Reflection shellResolution: 1.08→1.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 21595 / CC1/2: 0.893 / Rpim(I) all: 0.199 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
SCALA3.3.20data scaling
MOLREP11.0.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MXC
Resolution: 1.08→17.61 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.567 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.021 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12788 7610 5 %RANDOM
Rwork0.11695 ---
obs0.1175 143739 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 8.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20.37 Å2
2---0.43 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.08→17.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 97 488 2931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0142697
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182336
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.6853709
X-RAY DIFFRACTIONr_angle_other_deg0.9311.6875510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4955361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69321.969127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80615402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7061515
X-RAY DIFFRACTIONr_chiral_restr0.0590.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
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_it0.5530.7381297
X-RAY DIFFRACTIONr_mcbond_other0.5520.7381296
X-RAY DIFFRACTIONr_mcangle_it0.8211.1161633
X-RAY DIFFRACTIONr_mcangle_other0.8221.1161634
X-RAY DIFFRACTIONr_scbond_it0.5880.8361399
X-RAY DIFFRACTIONr_scbond_other0.5880.8361399
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7741.2162050
X-RAY DIFFRACTIONr_long_range_B_refined2.25110.2923223
X-RAY DIFFRACTIONr_long_range_B_other1.5689.1073060
X-RAY DIFFRACTIONr_rigid_bond_restr0.64135032
X-RAY DIFFRACTIONr_sphericity_free17.4075293
X-RAY DIFFRACTIONr_sphericity_bonded5.97855151
LS refinement shellResolution: 1.08→1.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 507 -
Rwork0.221 10387 -
obs--96.23 %

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