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- PDB-1qmj: CG-16, a homodimeric agglutinin from chicken liver -

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Basic information

Entry
Database: PDB / ID: 1qmj
TitleCG-16, a homodimeric agglutinin from chicken liver
ComponentsBETA-GALACTOSIDE-BINDING LECTIN
KeywordsSUGAR BINDING PROTEIN / GALECTIN
Function / homology
Function and homology information


lactose binding / laminin binding / extracellular space
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-MERCAPTOETHANOL / 16 kDa beta-galactoside-binding lectin
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsVarela, P.F. / Solis, D. / Diaz-Maurino, T. / Kaltner, H. / Gabius, H.-J. / Romero, A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The 2.15 A Crystal Structure of Cg-16, the Developmentally Regulated Homodimeric Chicken Galectin
Authors: Varela, P.F. / Solis, D. / Diaz-Maurino, T. / Kaltner, H. / Gabius, H.-J. / Romero, A.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1976
Title: Developmentally Regulated Lectin in Embryonic Chick Muscle and a Myogenic Cell Line
Authors: Nowak, T.P. / Haywood, P.L. / Barondes, S.H.
History
DepositionSep 29, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2000Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE ANTI-PARALLEL BETA-SHEET STRUCTURE OF EACH MONOMER IS ... SHEET DETERMINATION METHOD: DSSP THE ANTI-PARALLEL BETA-SHEET STRUCTURE OF EACH MONOMER IS EXTENDED AS THE TWO MONOMERS ASSOCIATE TO FORM A DIMER CONTAINING AN EXTENDED BETA-SANDWICH, EACH WITH THE SAME JELLY ROLL TOPOLOGY. STRANDS 1 OF EACH SHEET A1 AND B1 ARE CONNECTED AS ARE STRANS 5 OF EACH SHEET A2 AND B2. THE SHEET IS HOWEVER, PRESENT HERE PER MONOMER ONLY. THE SHEET STRUCTURE OF THIS MOLECULE IS ALSO BIFURCATED, WITH STRAND 5 OF SHEET A1 (B1) CONNECTED TO STRAND 1 OF SHEET A3 (B3).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-GALACTOSIDE-BINDING LECTIN
B: BETA-GALACTOSIDE-BINDING LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6986
Polymers29,3852
Non-polymers3134
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-12.3 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.380, 82.600, 112.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.95636, -0.28284, 0.07327), (-0.27938, 0.81182, -0.51273), (0.08554, -0.51083, -0.85542)
Vector: 31.39846, 41.13992, 128.37543)

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Components

#1: Protein BETA-GALACTOSIDE-BINDING LECTIN / 16 KD LECTIN / C-16


Mass: 14692.690 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / Organ: LIVER / References: UniProt: P23668
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE NUMBERING IS MADE ACCORDING TO THE BOVINE GAL-1 STRUCTURE. THERE IS A GAP BETWEEN RESIDUES ...THE NUMBERING IS MADE ACCORDING TO THE BOVINE GAL-1 STRUCTURE. THERE IS A GAP BETWEEN RESIDUES GLU102 AND VAL104 - MAXIMIZE THE STRUCTURAL ALIGNMENT.
Sequence detailsRESIDUES MET1 AND GLU2 ARE NOT MODELLED. NUMBERING IN THE PDB DATA BASE IS MADE ACCORDING TO THE ...RESIDUES MET1 AND GLU2 ARE NOT MODELLED. NUMBERING IN THE PDB DATA BASE IS MADE ACCORDING TO THE GAL-1 BOVINE STRUCTURE. THIS NUMBERING GIVES A GAP BETWEEN RESIDUES 102 AND 104.

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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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion / pH: 5.6
Details: CRYSTALS WERE OBTAINED IN HANGING OR SITTING DROPS BY MIXING EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) AND THE PRECIPITATING BUFFER (2M AMMONIUM SULPHATE, 5% (V/V) ISOPROPANOL AND 1% ...Details: CRYSTALS WERE OBTAINED IN HANGING OR SITTING DROPS BY MIXING EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) AND THE PRECIPITATING BUFFER (2M AMMONIUM SULPHATE, 5% (V/V) ISOPROPANOL AND 1% BETA-MERCAPTO ETHANOL, PH 5.6)
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.2 / Method: vapor diffusion
Details: drop consists of equal volume of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
25 mMsodium phosphate1drop
30.2 M1dropNaCl
40.1 Mlactose1drop
54 mMbeta-mercaptoethanol1drop
62 Mammonium sulfate1reservoirprecipitant
75 %(v/v)isopropanol1reservoirprecipitant
81 %beta-mercaptoethanol1reservoirprecipitant

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 15244 / % possible obs: 87.8 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.0307 / Rsym value: 0.056 / Net I/σ(I): 7.8
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.0451 / Mean I/σ(I) obs: 4 / Rsym value: 0.204 / % possible all: 75
Reflection
*PLUS
Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 75 % / Rmerge(I) obs: 0.204

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SLA

1sla


Resolution: 2.15→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1051 7 %RANDOM
Rwork0.185 ---
obs0.185 15047 87.5 %-
Displacement parametersBiso mean: 33.6 Å2
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 16 130 2208
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.477
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.127
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.31.5
X-RAY DIFFRACTIONx_mcangle_it2.12
X-RAY DIFFRACTIONx_scbond_it2.22
X-RAY DIFFRACTIONx_scangle_it2.82.5
LS refinement shellResolution: 2.15→2.25 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.311 119 7 %
Rwork0.294 1522 -
obs--65 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX.PROTOPHCSD.PRO
X-RAY DIFFRACTION2SEO.PARAMSEO.TOP

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