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- PDB-5nm1: Chicken GRIFIN (crystallisation pH: 6.2) -

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Basic information

Entry
Database: PDB / ID: 5nm1
TitleChicken GRIFIN (crystallisation pH: 6.2)
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: 2.099 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 5, 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 / chem_comp ...atom_site / 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 / _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
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin
B: Galectin
C: Galectin
D: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1918
Polymers64,8224
Non-polymers1,3694
Water3,315184
1
D: Galectin
hetero molecules

A: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0954
Polymers32,4112
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1/2,z+1/21
2
A: Galectin
hetero molecules

D: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0954
Polymers32,4112
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544-x,-y-1/2,z-1/21
Buried area2290 Å2
ΔGint-1 kcal/mol
Surface area13160 Å2
MethodPISA
3
B: Galectin
C: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0954
Polymers32,4112
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-2 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.873, 103.930, 129.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Galectin


Mass: 16205.410 Da / Num. of mol.: 4
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.: 4
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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 20% PEG 1K, 0.1M Na/K Phosphate pH 6.2, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.099→48.223 Å / Num. obs: 35607 / % possible obs: 98.2 % / Redundancy: 2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.048 / Net I/σ(I): 6.72
Reflection shellResolution: 2.099→2.17 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.24 / Num. unique obs: 3189 / CC1/2: 0.672 / % possible all: 89.91

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NLD

5nld


Resolution: 2.099→48.223 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.96
RfactorNum. reflection% reflection
Rfree0.2802 1778 5 %
Rwork0.213 --
obs0.2164 35589 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.099→48.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 92 184 4749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074698
X-RAY DIFFRACTIONf_angle_d0.9636355
X-RAY DIFFRACTIONf_dihedral_angle_d13.7622744
X-RAY DIFFRACTIONf_chiral_restr0.057693
X-RAY DIFFRACTIONf_plane_restr0.006804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0994-2.15620.40261270.33342271X-RAY DIFFRACTION87
2.1562-2.21960.35151130.29122578X-RAY DIFFRACTION99
2.2196-2.29120.39171320.27122591X-RAY DIFFRACTION100
2.2912-2.37310.32141500.27252604X-RAY DIFFRACTION100
2.3731-2.46810.33331380.26442599X-RAY DIFFRACTION100
2.4681-2.58050.34991270.24632582X-RAY DIFFRACTION99
2.5805-2.71650.32021510.24762611X-RAY DIFFRACTION100
2.7165-2.88670.32881410.26032617X-RAY DIFFRACTION99
2.8867-3.10950.31051250.24152620X-RAY DIFFRACTION99
3.1095-3.42240.32621400.22432620X-RAY DIFFRACTION98
3.4224-3.91740.25771460.19262632X-RAY DIFFRACTION99
3.9174-4.93480.21221440.15412665X-RAY DIFFRACTION98
4.9348-48.23570.22441440.18132821X-RAY DIFFRACTION99

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