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- PDB-4uw6: Human galectin-7 in complex with a galactose based dendron D3 -

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Basic information

Entry
Database: PDB / ID: 4uw6
TitleHuman galectin-7 in complex with a galactose based dendron D3
ComponentsGALECTIN-7
KeywordsSUGAR BINDING PROTEIN / LECTIN / DENDRIMERS / MULTIVALENCY / CARBOHYDRATE BINDING
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / 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
DENDRON-D3 / Galectin-7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsRamaswamy, S. / Sleiman, M.H. / Masuyer, G. / Arbez-Gindre, C. / Micha-Screttas, M. / Calogeropoulou, T. / Steele, B.R. / Acharya, K.R.
CitationJournal: FEBS J. / Year: 2015
Title: Structural Basis of Multivalent Galactose-Based Dendrimer Recognition by Human Galectin-7.
Authors: Ramaswamy, S. / Haj Sleiman, M. / Masuyer, G. / Arbez-Gindre, C. / Micha-Screttas, M. / Calogeropoulou, T. / Steele, B.R. / Acharya, K.R.
History
DepositionAug 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_initial_refinement_model / pdbx_validate_chiral / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GALECTIN-7
B: GALECTIN-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0053
Polymers30,1942
Non-polymers1,8101
Water2,810156
1
A: GALECTIN-7


Theoretical massNumber of molelcules
Total (without water)15,0971
Polymers15,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GALECTIN-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9082
Polymers15,0971
Non-polymers1,8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.930, 53.380, 89.220
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-2043-

HOH

21A-2092-

HOH

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Components

#1: Protein GALECTIN-7 / GAL-7 / HKL-14 / PI7 / P53-INDUCED GENE 1 PROTEIN


Mass: 15097.046 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P47929
#2: Chemical ChemComp-VV7 / DENDRON-D3


Mass: 1810.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H77N20O39
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.14 Å3/Da / Density % sol: 42.49 % / Description: NONE
Crystal growDetails: 0.05M BISTRIS PROPANE PH7, 17% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.79→45.49 Å / Num. obs: 24387 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.2
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.4 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BKZ

1bkz


Resolution: 1.79→45.495 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 27.08 / Stereochemistry target values: ML
Details: RESIDUES 1-4 ARE DISORDERED ELECTRON DENSITY FOR ONLY FOUR OF SIX ARMS FOR THE DENDRON IS OBSERVED. PDB FILE CONTAINS ONLY THESE FOUR ARMS.
RfactorNum. reflection% reflection
Rfree0.2509 1247 5.1 %
Rwork0.2002 --
obs0.2028 24359 95.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→45.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 95 156 2318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122249
X-RAY DIFFRACTIONf_angle_d1.4373059
X-RAY DIFFRACTIONf_dihedral_angle_d15.538965
X-RAY DIFFRACTIONf_chiral_restr0.147322
X-RAY DIFFRACTIONf_plane_restr0.007408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.86170.30641300.24432432X-RAY DIFFRACTION91
1.8617-1.94640.25111690.21432535X-RAY DIFFRACTION95
1.9464-2.04910.26811350.20862583X-RAY DIFFRACTION96
2.0491-2.17740.29591260.20442590X-RAY DIFFRACTION96
2.1774-2.34550.25561250.21372510X-RAY DIFFRACTION93
2.3455-2.58160.23511190.21312683X-RAY DIFFRACTION98
2.5816-2.95510.29151390.22912607X-RAY DIFFRACTION97
2.9551-3.72280.251360.19262559X-RAY DIFFRACTION94
3.7228-45.50930.221680.1712613X-RAY DIFFRACTION95

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