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- PDB-5nld: Chicken GRIFIN (crystallisation pH: 7.5) -

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Basic information

Entry
Database: PDB / ID: 5nld
TitleChicken GRIFIN (crystallisation pH: 7.5)
ComponentsGalectin
KeywordsSUGAR BINDING PROTEIN / Galectin related protein
Function / homology
Function and homology information


carbohydrate binding / cytoplasm
Similarity search - Function
Grifin / 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 ...Grifin / 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
alpha-lactose / Galectin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsRuiz, F.M. / Romero, A.
Funding support1items
OrganizationGrant numberCountry
European Union317297 (GLYCOPHARM)
CitationJournal: Biochimie / Year: 2018
Title: Chicken GRIFIN: Structural characterization in crystals and in solution.
Authors: Ruiz, F.M. / Gilles, U. / Ludwig, A.K. / Sehad, C. / Shiao, T.C. / Garcia Caballero, G. / Kaltner, H. / Lindner, I. / Roy, R. / Reusch, D. / Romero, A. / Gabius, H.J.
History
DepositionApr 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin
B: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7533
Polymers32,4112
Non-polymers3421
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-2 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.146, 60.736, 53.878
Angle α, β, γ (deg.)90.00, 92.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Galectin /


Mass: 16205.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: GRIFIN / Production host: Escherichia coli (E. coli) / References: UniProt: F1NZ18
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5% w/v 2-Propanol, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9599 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9599 Å / Relative weight: 1
ReflectionResolution: 0.96→39.11 Å / Num. obs: 148722 / % possible obs: 97.04 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 15.02
Reflection shellResolution: 0.96→0.99 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 13666 / CC1/2: 0.82 / % possible all: 89.78

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Theoretical model

Resolution: 0.96→39.11 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.84
RfactorNum. reflection% reflection
Rfree0.1494 7397 4.97 %
Rwork0.1368 --
obs0.1374 148709 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.96→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 23 296 2570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092427
X-RAY DIFFRACTIONf_angle_d1.4893307
X-RAY DIFFRACTIONf_dihedral_angle_d14.74911
X-RAY DIFFRACTIONf_chiral_restr0.118360
X-RAY DIFFRACTIONf_plane_restr0.008424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.96-0.97090.23661950.23554084X-RAY DIFFRACTION84
0.9709-0.98230.22892290.20844401X-RAY DIFFRACTION91
0.9823-0.99430.18882590.19134496X-RAY DIFFRACTION94
0.9943-1.00690.2082430.17284610X-RAY DIFFRACTION95
1.0069-1.02020.16672420.15464638X-RAY DIFFRACTION95
1.0202-1.03410.16792550.1444610X-RAY DIFFRACTION96
1.0341-1.04890.15052220.13694673X-RAY DIFFRACTION96
1.0489-1.06460.12772350.12444639X-RAY DIFFRACTION96
1.0646-1.08120.1372350.12284662X-RAY DIFFRACTION96
1.0812-1.09890.11582460.11654711X-RAY DIFFRACTION97
1.0989-1.11790.13172490.1124646X-RAY DIFFRACTION97
1.1179-1.13820.12192640.10774653X-RAY DIFFRACTION97
1.1382-1.16010.12582700.10744683X-RAY DIFFRACTION97
1.1601-1.18380.12012410.10884689X-RAY DIFFRACTION97
1.1838-1.20950.13582510.11274718X-RAY DIFFRACTION97
1.2095-1.23770.13422300.11014716X-RAY DIFFRACTION98
1.2377-1.26860.12932570.11214757X-RAY DIFFRACTION98
1.2686-1.30290.12762540.11434762X-RAY DIFFRACTION98
1.3029-1.34130.12932370.11734790X-RAY DIFFRACTION99
1.3413-1.38450.14522320.11794809X-RAY DIFFRACTION99
1.3845-1.4340.12792600.12354762X-RAY DIFFRACTION99
1.434-1.49150.12922600.12344819X-RAY DIFFRACTION99
1.4915-1.55930.14493030.12134770X-RAY DIFFRACTION99
1.5593-1.64150.13282660.13044866X-RAY DIFFRACTION100
1.6415-1.74440.16222480.13854839X-RAY DIFFRACTION100
1.7444-1.87910.1432480.14094886X-RAY DIFFRACTION100
1.8791-2.06820.14632310.13644912X-RAY DIFFRACTION100
2.0682-2.36740.16492470.14614832X-RAY DIFFRACTION100
2.3674-2.98250.17692440.15994913X-RAY DIFFRACTION100
2.9825-39.1440.15462440.14734966X-RAY DIFFRACTION100

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