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- PDB-4agg: Structure of a tetrameric galectin from Cinachyrella sp. (Ball sponge) -

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Basic information

Entry
Database: PDB / ID: 4agg
TitleStructure of a tetrameric galectin from Cinachyrella sp. (Ball sponge)
ComponentsGALECTIN
KeywordsCARBOHYDRATE-BINDING PROTEIN / GALECTIN
Function / homology
Function and homology information


carbohydrate binding
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 speciesCINACHYRELLA SP. (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsFreymann, D.M. / Focia, P.J. / Sakai, R. / Swanson, G.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of a Tetrameric Galectin from Cinachyrella Sp. (Ball Sponge).
Authors: Freymann, D.M. / Nakamura, Y. / Focia, P.J. / Sakai, R. / Swanson, G.T.
History
DepositionJan 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GALECTIN
B: GALECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1843
Polymers32,1482
Non-polymers351
Water48627
1
A: GALECTIN
B: GALECTIN
hetero molecules

A: GALECTIN
B: GALECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3676
Polymers64,2964
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5150 Å2
ΔGint-24.8 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.005, 126.635, 80.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GALECTIN


Mass: 16074.089 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) CINACHYRELLA SP. (invertebrata) / References: UniProt: I0IV54*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.5 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5, 30% PEG3000

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.98→49.75 Å / Num. obs: 6308 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.7
Reflection shellResolution: 2.98→3.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 74.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IS5, SIDECHAINS TRUNCATED

1is5


Resolution: 2.98→40.22 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.854 / SU B: 24.079 / SU ML: 0.424 / Cross valid method: THROUGHOUT / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY TORSION ANGLE OUTLIERS IN THE STRUCTURE OCCUR FOR SOME RESIDUES IN POORLY DEFINED SURFACE LOOPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 295 4.7 %RANDOM
Rwork0.18622 ---
obs0.19042 5998 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.097 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.98→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 1 27 2278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022312
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9733148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.175286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72623.962106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.78815354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9961514
X-RAY DIFFRACTIONr_chiral_restr0.110.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211808
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.981→3.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 19 -
Rwork0.315 276 -
obs--63.03 %

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