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- PDB-1ule: CGL2 in complex with linear B2 trisaccharide -

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Basic information

Entry
Database: PDB / ID: 1ule
TitleCGL2 in complex with linear B2 trisaccharide
Componentsgalectin-2
KeywordsSUGAR BINDING PROTEIN / galectin / lectin / beta-galactoside binding lectin / sugar binding
Function / homology
Function and homology information


endomembrane system / carbohydrate binding / extracellular region / membrane
Similarity search - Function
Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWalser, P.J. / Haebel, P.W. / Kuenzler, M. / Kues, U. / Aebi, M. / Ban, N.
Citation
Journal: STRUCTURE / Year: 2004
Title: Structure and Functional Analysis of the Fungal Galectin CGL2
Authors: Walser, P.J. / Haebel, P.W. / Kuenzler, M. / Sargent, D. / Kues, U. / Aebi, M. / Ban, N.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1998
Title: Crystallography & NMR system: A new software suite for macromolecular structure determination.
Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / DeLano, W.L. / Gros, P. / Grosse-Kunstleve, R.W. / Jiang, J.S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G.L.
History
DepositionSep 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: galectin-2
B: galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6254
Polymers33,5342
Non-polymers1,0912
Water5,332296
1
A: galectin-2
B: galectin-2
hetero molecules

A: galectin-2
B: galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2508
Polymers67,0684
Non-polymers2,1824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area10680 Å2
ΔGint17 kcal/mol
Surface area25010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.315, 66.315, 218.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe galectin tetramer is generated from the dimer by a 2 fold rotation: -y, -x, -z+1/2

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Components

#1: Protein galectin-2 / / CGL2


Mass: 16766.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Gene: cgl2 / Plasmid: pYADE4 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): SEY 6210 / References: GenBank: 6983931, UniProt: Q9P4R8*PLUS
#2: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.12 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 3350, PEG 400, sodium phosphate, sodium chloride, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9998 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.15→49.03 Å / Num. all: 26251 / Num. obs: 27145 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 25 Å2 / Limit h max: 30 / Limit h min: 0 / Limit k max: 21 / Limit k min: 0 / Limit l max: 101 / Limit l min: 0 / Observed criterion F max: 585892.71 / Observed criterion F min: 0.55 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 32.2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.5 % / Num. unique all: 2670 / Rsym value: 0.254 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CGL2-Lactose

Resolution: 2.15→49.03 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1285 4.9 %RANDOM
Rwork0.198 ---
all-26251 --
obs-26251 95.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 63.1547 Å2 / ksol: 0.355203 e/Å3
Displacement parametersBiso max: 79.3 Å2 / Biso mean: 34.94 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1-3.37 Å20 Å20 Å2
2--3.37 Å20 Å2
3----6.75 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Luzzati d res high-2.15
Refinement stepCycle: LAST / Resolution: 2.15→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 74 296 2746
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg26.4
X-RAY DIFFRACTIONc_torsion_impr_deg0.76
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.15-2.250.2491334.40.22328640.0223323299790.2
2.25-2.370.2871825.80.22629540.0213361313693.3
2.37-2.520.2471494.70.20630360.023348318595.1
2.52-2.710.2931514.70.22630820.0243371323395.9
2.71-2.990.2651624.90.22931360.0213401329896.9
2.99-3.420.2451855.50.20931850.0183417337098.6
3.42-4.310.1971484.30.17833060.0163475345499.4
4.31-49.030.2011754.90.1834030.0153696357896.8
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5cis_peptide.param

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