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- PDB-5h9s: Crystal Structure of Human Galectin-7 in Complex with TAZTDG -

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Basic information

Entry
Database: PDB / ID: 5h9s
TitleCrystal Structure of Human Galectin-7 in Complex with TAZTDG
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / galectin / thio-digalactoside (TDG) / pi-arginine interaction / fluorine bonding
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
Chem-TGZ / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.821 Å
AuthorsHsieh, T.J. / Lin, H.Y. / Lin, C.H.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Academia Sinica Taiwan
Ministry of Science and Technology102-2113-M-001-001-MY3 Taiwan
Ministry of Science and Technology102-2923-M-001-001-MY3 Taiwan
CitationJournal: Sci Rep / Year: 2016
Title: Dual thio-digalactoside-binding modes of human galectins as the structural basis for the design of potent and selective inhibitors
Authors: Hsieh, T.J. / Lin, H.Y. / Tu, Z. / Lin, T.C. / Wu, S.C. / Tseng, Y.Y. / Liu, F.T. / Danny Hsu, S.T. / Lin, C.H.
History
DepositionDec 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,7783
Polymers34,2742
Non-polymers5031
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint1 kcal/mol
Surface area12530 Å2
Unit cell
Length a, b, c (Å)53.873, 64.475, 73.046
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 Galectin-7 / Gal-7 / HKL-14 / PI7 / p53-induced gene 1 protein


Mass: 17137.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P47929
#2: Chemical ChemComp-TGZ / (2~{S},3~{R},4~{S},5~{R},6~{R})-2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-4-[4-(3-fluorophenyl)-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]sulfanyl-6-(hydroxymethyl)oxane-3,4,5-triol


Mass: 503.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26FN3O9S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.22 M MgAcetate, 21% (w/v) PEG 3350 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→30 Å / Num. obs: 23368 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 44.962
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.95 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKZ

1bkz


Resolution: 1.821→27.663 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 2000 8.57 %Random selection
Rwork0.1829 ---
obs0.1867 23331 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.821→27.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 34 83 2219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082191
X-RAY DIFFRACTIONf_angle_d1.1422973
X-RAY DIFFRACTIONf_dihedral_angle_d13.985825
X-RAY DIFFRACTIONf_chiral_restr0.055318
X-RAY DIFFRACTIONf_plane_restr0.006401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8215-1.8670.30261390.26141488X-RAY DIFFRACTION100
1.867-1.91750.261420.22881509X-RAY DIFFRACTION100
1.9175-1.97390.2371400.21221500X-RAY DIFFRACTION100
1.9739-2.03760.2511400.19551486X-RAY DIFFRACTION100
2.0376-2.11040.25011430.19011516X-RAY DIFFRACTION100
2.1104-2.19490.21161400.19631502X-RAY DIFFRACTION100
2.1949-2.29470.26491420.20441512X-RAY DIFFRACTION100
2.2947-2.41560.27031420.1891515X-RAY DIFFRACTION100
2.4156-2.56690.21481430.19571517X-RAY DIFFRACTION100
2.5669-2.76490.25741420.20621526X-RAY DIFFRACTION100
2.7649-3.04280.23491460.20271546X-RAY DIFFRACTION100
3.0428-3.48240.24121430.18291540X-RAY DIFFRACTION100
3.4824-4.38460.1931460.16351556X-RAY DIFFRACTION100
4.3846-27.66610.21821520.16311618X-RAY DIFFRACTION98

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