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- PDB-1ulc: CGL2 in complex with lactose -

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Basic information

Entry
Database: PDB / ID: 1ulc
TitleCGL2 in complex with lactose
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
beta-lactose / : / Galectin-2
Similarity search - Component
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SAD (I), Molecular Replacement / Resolution: 2.6 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 / entity_name_com / 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_molecule_features / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,2184
Polymers33,5342
Non-polymers6852
Water1,910106
1
A: galectin-2
B: galectin-2
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)68,4378
Polymers67,0684
Non-polymers1,3694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9540 Å2
ΔGint0 kcal/mol
Surface area24610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.220, 65.220, 240.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsgalectin tetramer from crystallographic dimer by y, x, -z

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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): SEY6210 / References: GenBank: 6983931, UniProt: Q9P4R8*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.61 Å3/Da / Density % sol: 65.66 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→45.29 Å / Num. all: 16858 / Num. obs: 15351 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 57.1 Å2 / Limit h max: 25 / Limit h min: 0 / Limit k max: 17 / Limit k min: 0 / Limit l max: 92 / Limit l min: 0 / Observed criterion F max: 323811.85 / Observed criterion F min: 0.32 / Rsym value: 0.119 / Net I/σ(I): 20.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1375 / Rsym value: 0.372 / % possible all: 85.2

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD (I), Molecular Replacement
Resolution: 2.6→45.29 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1529 10 %random
Rwork0.21 ---
all-15351 --
obs-15351 91.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 31.6883 Å2 / ksol: 0.337492 e/Å3
Displacement parametersBiso max: 83.86 Å2 / Biso mean: 45.33 Å2 / Biso min: 11.58 Å2
Baniso -1Baniso -2Baniso -3
1-11.48 Å20 Å20 Å2
2--11.48 Å20 Å2
3----22.96 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.48 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→45.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 46 106 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg26.2
X-RAY DIFFRACTIONc_torsion_impr_deg0.88
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.732.5
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 (%)
2.6-2.720.41115310.50.38713050.0332046145871.3
2.72-2.860.4191679.40.35916040.0322047177186.5
2.86-3.040.3651638.80.27916850.0292039184890.6
3.04-3.280.3291859.60.27517430.0242069192893.2
3.28-3.610.30920010.10.24217790.0222090197994.7
3.61-4.130.241849.10.18518300.0182099201496
4.13-5.20.188232110.13318690.0122141210198.1
5.2-45.290.23324510.90.17820070.0152297225298
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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