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- PDB-7p8h: chicken GRIFIN bound to blood group tetrasaccharide B (type 1) -

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Basic information

Entry
Database: PDB / ID: 7p8h
Titlechicken GRIFIN bound to blood group tetrasaccharide B (type 1)
ComponentsGalectin
KeywordsSUGAR BINDING PROTEIN / GRIFIN / Galactoside-binding lectin / Blood group B type 1 antigen / beta anomer
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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsRuiz, F.M. / Romero, A.
CitationJournal: Biomolecules / Year: 2021
Title: Structural Characterization of Rat Galectin-5, an N-Tailed Monomeric Proto-Type-like Galectin.
Authors: Ruiz, F.M. / Medrano, F.J. / Ludwig, A.K. / Kaltner, H. / Shilova, N.V. / Bovin, N.V. / Gabius, H.J. / Romero, A.
History
DepositionJul 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin
C: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7944
Polymers32,4112
Non-polymers1,3832
Water8,683482
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint31 kcal/mol
Surface area12800 Å2
Unit cell
Length a, b, c (Å)39.104, 70.554, 87.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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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 BL21(DE3) (bacteria) / References: UniProt: F1NZ18
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-2-acetamido- ...alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 691.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Blood group B type 1 antigen, beta anomer / References: BIRD: PRD_002353
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5]/1-2-3-4/a3-b1_b2-c1_b3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O
Compound detailsB Type 1, blood group B type 1 tetrasaccharide, alpha-D-Galp-(1->3)-[alpha-L-Fucp-(1->2)]-beta-D- ...B Type 1, blood group B type 1 tetrasaccharide, alpha-D-Galp-(1->3)-[alpha-L-Fucp-(1->2)]-beta-D-Galp-(1->3)-beta-D-GlcpNAc
Has ligand of interestY

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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: 1.87 Å3/Da / Density % sol: 34.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 15 % w/v Polyethylene glycol 400; 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.13→43.85 Å / Num. obs: 90857 / % possible obs: 99.13 % / Redundancy: 2 % / Biso Wilson estimate: 9.99 Å2 / CC1/2: 0.9 / Rmerge(I) obs: 0.015 / Rrim(I) all: 0.021 / Net I/σ(I): 22
Reflection shellResolution: 1.13→1.17 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2 / Num. unique obs: 8884 / CC1/2: 0.9 / Rrim(I) all: 0.431

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NMJ

5nmj


Resolution: 1.13→43.85 Å / SU ML: 0.1521 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.176 4580 5.04 %
Rwork0.1535 86223 -
obs0.1546 90803 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.52 Å2
Refinement stepCycle: LAST / Resolution: 1.13→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 94 482 2846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792530
X-RAY DIFFRACTIONf_angle_d1.08883454
X-RAY DIFFRACTIONf_chiral_restr0.0932388
X-RAY DIFFRACTIONf_plane_restr0.009432
X-RAY DIFFRACTIONf_dihedral_angle_d14.3569925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.140.51151360.57082779X-RAY DIFFRACTION96.78
1.14-1.160.47761410.43822802X-RAY DIFFRACTION97.51
1.16-1.170.3721400.35252852X-RAY DIFFRACTION98.91
1.17-1.190.34061430.2932794X-RAY DIFFRACTION96.68
1.19-1.20.25561380.25022849X-RAY DIFFRACTION99.73
1.2-1.220.2471460.20912795X-RAY DIFFRACTION97.87
1.22-1.230.24781580.18662816X-RAY DIFFRACTION98.77
1.23-1.250.22131430.17022861X-RAY DIFFRACTION99.31
1.25-1.270.20111400.16442813X-RAY DIFFRACTION98.3
1.27-1.290.16461730.16172847X-RAY DIFFRACTION99.64
1.29-1.320.22081520.17112816X-RAY DIFFRACTION98.41
1.32-1.340.20811310.16572896X-RAY DIFFRACTION99.54
1.34-1.370.20711330.17262848X-RAY DIFFRACTION98.68
1.37-1.390.23341350.16992896X-RAY DIFFRACTION99.41
1.39-1.420.18811580.17172828X-RAY DIFFRACTION99.24
1.42-1.460.20131560.16232869X-RAY DIFFRACTION99.28
1.46-1.490.16731770.14372867X-RAY DIFFRACTION99.8
1.49-1.530.18191510.13492851X-RAY DIFFRACTION99.67
1.53-1.580.1791630.13082876X-RAY DIFFRACTION99.7
1.58-1.630.15261760.12622882X-RAY DIFFRACTION99.61
1.63-1.690.14881630.13372865X-RAY DIFFRACTION99.87
1.69-1.760.1811620.13622901X-RAY DIFFRACTION99.77
1.76-1.840.19681500.13992896X-RAY DIFFRACTION99.9
1.84-1.930.1661460.13742919X-RAY DIFFRACTION99.93
1.93-2.050.16631620.13452920X-RAY DIFFRACTION99.9
2.05-2.210.14021670.12892906X-RAY DIFFRACTION99.71
2.21-2.430.14831490.13942916X-RAY DIFFRACTION99.06
2.43-2.790.16071550.14562968X-RAY DIFFRACTION99.94
2.79-3.510.14091640.1362999X-RAY DIFFRACTION100
3.51-43.850.16091720.14443096X-RAY DIFFRACTION99.03

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