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- PDB-5nm6: Chicken GRIFIN (crystallisation pH: 4.6) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5nm6
TitleChicken GRIFIN (crystallisation pH: 4.6)
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.458 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin
B: Galectin


Theoretical massNumber of molelcules
Total (without water)32,4112
Polymers32,4112
Non-polymers00
Water5,477304
1
A: Galectin

B: Galectin


Theoretical massNumber of molelcules
Total (without water)32,4112
Polymers32,4112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area1590 Å2
ΔGint-4 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)38.943, 60.274, 54.145
Angle α, β, γ (deg.)90.00, 92.47, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30%PEG4K, Na Acetate 0.1M pH 4.6, 0.2M Amm. Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.458→40.26 Å / Num. obs: 39758 / % possible obs: 90.98 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 15.18
Reflection shellResolution: 1.458→1.51 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 3661 / % possible all: 84.47

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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
Resolution: 1.458→40.259 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.89
RfactorNum. reflection% reflection
Rfree0.2174 1977 4.97 %
Rwork0.1763 --
obs0.1783 39747 90.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.458→40.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 0 304 2563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062379
X-RAY DIFFRACTIONf_angle_d0.8463227
X-RAY DIFFRACTIONf_dihedral_angle_d3.0381708
X-RAY DIFFRACTIONf_chiral_restr0.094340
X-RAY DIFFRACTIONf_plane_restr0.006419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4576-1.49410.35551230.31992418X-RAY DIFFRACTION82
1.4941-1.53450.27821590.26942726X-RAY DIFFRACTION94
1.5345-1.57970.27131460.22282797X-RAY DIFFRACTION95
1.5797-1.63060.26361410.21372854X-RAY DIFFRACTION95
1.6306-1.68890.24591520.21212787X-RAY DIFFRACTION95
1.6889-1.75650.25931370.20032796X-RAY DIFFRACTION94
1.7565-1.83650.22511340.19832761X-RAY DIFFRACTION94
1.8365-1.93330.22181610.17612763X-RAY DIFFRACTION93
1.9333-2.05440.20141350.16442740X-RAY DIFFRACTION93
2.0544-2.21310.21061640.16332672X-RAY DIFFRACTION91
2.2131-2.43570.21271500.17232704X-RAY DIFFRACTION91
2.4357-2.78810.23921370.17392646X-RAY DIFFRACTION89
2.7881-3.51240.17911240.15552592X-RAY DIFFRACTION87
3.5124-40.2740.18611140.14712514X-RAY DIFFRACTION82

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