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- PDB-6n3r: Sheep Galectin-11 (LGALS11) complex with galactose -

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Basic information

Entry
Database: PDB / ID: 6n3r
TitleSheep Galectin-11 (LGALS11) complex with galactose
ComponentsGalectin
KeywordsSUGAR BINDING PROTEIN / Glycan binding / Galectin / Lectin
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Galectin-10 / 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 ...Galectin-10 / 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-D-galactopyranose / Galectin
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.397 Å
AuthorsBeddoe, T.C. / Sakthivel, D.
Citation
Journal: To be Published
Title: Sheep Galectin-11 (LGALS11) complex with galactose
Authors: Beddoe, T.C. / Sakthivel, D.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Cloning, expression, purification and crystallographic studies of galectin-11 from domestic sheep (Ovis aries).
Authors: Sakthivel, D. / Littler, D. / Shahine, A. / Troy, S. / Johnson, M. / Rossjohn, J. / Piedrafita, D. / Beddoe, T.
History
DepositionNov 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin
B: Galectin
C: Galectin
D: Galectin
E: Galectin
F: Galectin
G: Galectin
H: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,54813
Polymers124,6478
Non-polymers9015
Water19,1681064
1
A: Galectin
E: Galectin


Theoretical massNumber of molelcules
Total (without water)31,1622
Polymers31,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-18 kcal/mol
Surface area13120 Å2
MethodPISA
2
B: Galectin
D: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5224
Polymers31,1622
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-15 kcal/mol
Surface area12760 Å2
MethodPISA
3
C: Galectin
hetero molecules

H: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5224
Polymers31,1622
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_847-x+3,y-1/2,-z+5/21
Buried area1610 Å2
ΔGint-15 kcal/mol
Surface area12600 Å2
MethodPISA
4
F: Galectin
hetero molecules

G: Galectin


Theoretical massNumber of molelcules
Total (without water)31,3423
Polymers31,1622
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x+1/2,-y+5/2,-z+21
Buried area1270 Å2
ΔGint-17 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.110, 127.430, 140.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Galectin / / Galectin-11


Mass: 15580.910 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Strain: Merino / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0A7EMW6
#2: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1064 / 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: 3.45 Å3/Da / Density % sol: 64.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% v/v Tacsimate, pH 7.0, 0.1 M HEPES, pH 7.5, 20% w/v PEG3350
PH range: 7.3 - 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 6, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.397→47.169 Å / Num. obs: 68286 / % possible obs: 99.97 % / Redundancy: 7.9 % / Biso Wilson estimate: 22.3 Å2 / Net I/σ(I): 7.3
Reflection shellResolution: 2.71→2.81 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.10_2148refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.397→47.169 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 3454 5.06 %
Rwork0.1604 64797 -
obs0.1629 68251 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.18 Å2 / Biso mean: 24.3736 Å2 / Biso min: 7.79 Å2
Refinement stepCycle: final / Resolution: 2.397→47.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8494 0 60 1064 9618
Biso mean--42.57 30.02 -
Num. residues----1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078797
X-RAY DIFFRACTIONf_angle_d0.89911971
X-RAY DIFFRACTIONf_chiral_restr0.0541358
X-RAY DIFFRACTIONf_plane_restr0.0061534
X-RAY DIFFRACTIONf_dihedral_angle_d14.7945238
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.397-2.42980.28351330.19425712704100
2.4298-2.46450.25321310.196825662697100
2.4645-2.50130.27061370.190125662703100
2.5013-2.54040.26371330.191225592692100
2.5404-2.58210.22111480.187725302678100
2.5821-2.62660.25051170.185825802697100
2.6266-2.67430.26371210.185525802701100
2.6743-2.72580.23481370.181725662703100
2.7258-2.78140.24021400.183625542694100
2.7814-2.84190.24181330.181225982731100
2.8419-2.9080.21271520.176625532705100
2.908-2.98070.24311500.169825392689100
2.9807-3.06130.23341510.170925802731100
3.0613-3.15130.23351350.169825732708100
3.1513-3.2530.19811290.166225942723100
3.253-3.36930.21211260.164425872713100
3.3693-3.50410.21161290.154725912720100
3.5041-3.66350.21191590.158225862745100
3.6635-3.85660.18911350.149626082743100
3.8566-4.09810.17721350.137126062741100
4.0981-4.41430.15461370.124126112748100
4.4143-4.85810.12821400.106226342774100
4.8581-5.56020.19041380.13126322770100
5.5602-7.00150.19421510.169826682819100
7.0015-47.17830.22421570.18452765292299

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