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- PDB-4uw5: Human galectin-7 in complex with a galactose based dendron D2-2. -

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Basic information

Entry
Database: PDB / ID: 4uw5
TitleHuman galectin-7 in complex with a galactose based dendron D2-2.
ComponentsHUMAN GALECTIN-7
KeywordsSUGAR BINDING PROTEIN / LECTIN / DENDRIMERS / MULTIVALENCY / CARBOHYDRATE BINDING
Function / homology
Function and homology information


Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / heterophilic cell-cell adhesion / 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 D2-1 / Galectin-7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 1.2Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN GALECTIN-7
B: HUMAN GALECTIN-7
C: HUMAN GALECTIN-7
D: HUMAN GALECTIN-7
E: HUMAN GALECTIN-7
F: HUMAN GALECTIN-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2578
Polymers90,5826
Non-polymers2,6742
Water7,602422
1
A: HUMAN GALECTIN-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4342
Polymers15,0971
Non-polymers1,3371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HUMAN GALECTIN-7


Theoretical massNumber of molelcules
Total (without water)15,0971
Polymers15,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HUMAN GALECTIN-7


Theoretical massNumber of molelcules
Total (without water)15,0971
Polymers15,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HUMAN GALECTIN-7


Theoretical massNumber of molelcules
Total (without water)15,0971
Polymers15,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: HUMAN GALECTIN-7


Theoretical massNumber of molelcules
Total (without water)15,0971
Polymers15,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: HUMAN GALECTIN-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4342
Polymers15,0971
Non-polymers1,3371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.440, 115.650, 116.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15097.046 Da / Num. of mol.: 6
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-4S0 / DENDRON D2-1


Mass: 1337.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H80N10O33
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.22 Å3/Da / Density % sol: 44.6 % / Description: NONE
Crystal growDetails: 0.05M BIS TRIS PROPANE PH7, 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9783
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 2.04→55.69 Å / Num. obs: 54509 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 32.54 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.1
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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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: 2.04→55.687 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 36.18 / Stereochemistry target values: ML
Details: RESIDUES 1-3 ARE DISORDERED DENSITY MODIFICATION PERFORMED. MTZ FILE POST DENSITY MODIFICATION SUBMITTED.
RfactorNum. reflection% reflection
Rfree0.3185 1383 2.5 %
Rwork0.2376 --
obs0.2397 54463 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→55.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6234 0 184 422 6840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016597
X-RAY DIFFRACTIONf_angle_d1.4128957
X-RAY DIFFRACTIONf_dihedral_angle_d15.3082753
X-RAY DIFFRACTIONf_chiral_restr0.056973
X-RAY DIFFRACTIONf_plane_restr0.0061186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.11290.38631400.31655259X-RAY DIFFRACTION99
2.1129-2.19750.4021350.29655251X-RAY DIFFRACTION99
2.1975-2.29750.38081260.29885253X-RAY DIFFRACTION99
2.2975-2.41870.38441210.26965320X-RAY DIFFRACTION99
2.4187-2.57020.37951310.26635264X-RAY DIFFRACTION99
2.5702-2.76870.30481510.26915298X-RAY DIFFRACTION99
2.7687-3.04730.36691440.26855244X-RAY DIFFRACTION98
3.0473-3.48810.31251310.2415365X-RAY DIFFRACTION99
3.4881-4.39440.29381430.20865340X-RAY DIFFRACTION98
4.3944-55.70820.27211610.19535486X-RAY DIFFRACTION97

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