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- PDB-1gzw: X-RAY CRYSTAL STRUCTURE OF HUMAN GALECTIN-1 -

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Basic information

Entry
Database: PDB / ID: 1gzw
TitleX-RAY CRYSTAL STRUCTURE OF HUMAN GALECTIN-1
Components(GALECTIN-1) x 2
KeywordsLECTIN / CARBOHYDRATE-BINDING PROTEINS / GALACTOSIDES / GALECTIN / CARBOHYDRATE-BINDING SITE
Function / homology
Function and homology information


galectin complex / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / carbohydrate binding ...galectin complex / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / carbohydrate binding / collagen-containing extracellular matrix / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / 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 / BETA-MERCAPTOETHANOL / Galectin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLopez-Lucendo, M.I.F. / Gabius, H.J. / Romero, A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Growth-Regulatory Human Galectin-1: Crystallographic Characterisation of the Structural Changes Induced by Single-Site Mutations and Their Impact on the Thermodynamics of Ligand Binding
Authors: Lopez-Lucendo, M.I.F. / Solis, D. / Andre, S. / Hirabayashi, J. / Kasai, K. / Kaltner, H. / Gabius, H.J. / Romero, A.
History
DepositionJun 7, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GALECTIN-1
B: GALECTIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,38610
Polymers29,2152
Non-polymers1,1718
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.979, 88.805, 93.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.40139, -0.37095, 0.83743), (-0.38053, -0.76413, -0.52087), (0.83312, -0.52773, 0.16556)
Vector: 43.90434, 110.70329, 18.67249)

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein GALECTIN-1 / / BETA-GALACTOSIDE-BINDING LECTIN L-14-I / LACTOSE-BINDING LECTIN 1 / S-LAC LECTIN 1 / GALAPTIN / 14 ...BETA-GALACTOSIDE-BINDING LECTIN L-14-I / LACTOSE-BINDING LECTIN 1 / S-LAC LECTIN 1 / GALAPTIN / 14 KDA LECTIN HPL / HBL


Mass: 14615.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PH14GAL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 / References: UniProt: P09382
#2: Protein GALECTIN-1 / / BETA-GALACTOSIDE-BINDING LECTIN L-14-I / LACTOSE-BINDING LECTIN 1 / S-LAC LECTIN 1 / GALAPTIN / 14 ...BETA-GALACTOSIDE-BINDING LECTIN L-14-I / LACTOSE-BINDING LECTIN 1 / S-LAC LECTIN 1 / GALAPTIN / 14 KDA LECTIN HPL / HBL


Mass: 14599.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PH14GAL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 / References: UniProt: P09382

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Sugars , 1 types, 2 molecules

#3: 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

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Non-polymers , 3 types, 290 molecules

#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.64 Å3/Da / Density % sol: 53.12 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5
Details: CRYSTALS WERE OBTAINED IN SITTING DROPS BY MIXING EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) AND THE PRECIPITATING BUFFER (2M AMMONIUM SULPHATE AND 1% BETA-MERCAPTO ETHANOL, PH 5.0)
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 Mammonium sulfate1reservoir
21 %beta-mercaptoethanol1reservoirpH5.6
320 mMsodium potassium phosphate1drop
45 mMlactose1droppH7.0
510 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.01
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 1.7→34.41 Å / Num. obs: 34966 / % possible obs: 96.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 5.8 / % possible all: 91.4
Reflection
*PLUS
Highest resolution: 1.7 Å / Redundancy: 3.9 % / Num. measured all: 209342 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 91.4 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 5.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SLT

1slt


Resolution: 1.7→34.41 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1383157.02 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1660 4.9 %RANDOM
Rwork0.216 ---
obs0.216 33538 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.2881 Å2 / ksol: 0.361596 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.09 Å20 Å20 Å2
2---5.46 Å20 Å2
3----0.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 71 284 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 264 5 %
Rwork0.301 5027 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4LACTOSA.PARAMLACTOSA.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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