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- PDB-4ndv: Crystal structure of L. decastes alpha-galactosyl-binding lectin ... -

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Basic information

Entry
Database: PDB / ID: 4ndv
TitleCrystal structure of L. decastes alpha-galactosyl-binding lectin in complex with globotriose
ComponentsAlpha-galactosyl-binding lectin
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology: / Alpha-galactosyl binding lectin / galactose binding / Alpha-galactosyl-binding lectin
Function and homology information
Biological speciesLyophyllum decastes (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVan Eerde, A. / Grahn, E. / Krengel, U.
CitationJournal: Glycobiology / Year: 2015
Title: Atomic-resolution structure of the alpha-galactosyl binding Lyophyllum decastes lectin reveals a new protein family found in both fungi and plants.
Authors: van Eerde, A. / Grahn, E.M. / Winter, H.C. / Goldstein, I.J. / Krengel, U.
History
DepositionOct 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / 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_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 / _pdbx_struct_assembly_gen.asym_id_list / _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.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 2.1Sep 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: Alpha-galactosyl-binding lectin
B: Alpha-galactosyl-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0873
Polymers20,5832
Non-polymers5041
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-8 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.870, 56.790, 44.500
Angle α, β, γ (deg.)90.000, 107.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-galactosyl-binding lectin


Mass: 10291.380 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lyophyllum decastes (fungus) / Organ: fruiting bodies / References: UniProt: A7UNK4
#2: Polysaccharide alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M calcium chloride, 0.1 M HEPES sodium, 28% v/v PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2007
RadiationMonochromator: diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.23→20 Å / Num. all: 48517 / Num. obs: 35328 / % possible obs: 71.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.76 Å2 / Rmerge(I) obs: 0.019 / Net I/σ(I): 26.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.23-1.30.2122.923694286118.5
1.3-1.390.134.639215637643.8
1.39-1.50.0788.1216251969371.9
1.5-1.650.05514.53253591164593.5
1.65-1.840.03322.46236261074895.1
1.84-2.120.0235.8220741949996.1
2.12-2.60.01547.8317623812596.8
2.6-3.660.01357.5413157615595.2
3.660.01261.686001301483.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NDS

4nds


Resolution: 1.3→19.641 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 17.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1555 1785 5.05 %RANDOM
Rwork0.1218 ---
all0.124 35328 --
obs0.1235 35321 86.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.2 Å2 / Biso mean: 14.403 Å2 / Biso min: 4.74 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 34 298 1776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091595
X-RAY DIFFRACTIONf_angle_d1.2332172
X-RAY DIFFRACTIONf_chiral_restr0.08231
X-RAY DIFFRACTIONf_plane_restr0.007284
X-RAY DIFFRACTIONf_dihedral_angle_d17.929599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.33510.2289670.13241193126040
1.3351-1.37430.1863840.12321511159552
1.3743-1.41870.1921950.11261908200363
1.4187-1.46940.17681270.10322272239977
1.4694-1.52820.15541400.10332775291592
1.5282-1.59770.15381440.100829603104100
1.5977-1.68190.18311520.106629793131100
1.6819-1.78720.16021280.111430003128100
1.7872-1.92510.15951780.125329603138100
1.9251-2.11860.15351730.114929653138100
2.1186-2.42470.16481440.122529883132100
2.4247-3.0530.16091670.134730143181100
3.053-19.64280.13331860.130730113197100

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