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- PDB-5vbk: Crystal structure of a galactose-binding Lectin from Mytilus cali... -

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Basic information

Entry
Database: PDB / ID: 5vbk
TitleCrystal structure of a galactose-binding Lectin from Mytilus californianus
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Galactose-Binding Lectin
Function / homologygalactose binding / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta / Galactose-binding lectin
Function and homology information
Biological speciesMytilus californianus (California mussel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.788 Å
AuthorsHernandez-Santoyo, A. / Garcia-Maldonado, E.
CitationJournal: Fish Shellfish Immunol. / Year: 2017
Title: Molecular and functional characterization of a glycosylated Galactose-Binding lectin from Mytilus californianus.
Authors: Garcia-Maldonado, E. / Cano-Sanchez, P. / Hernandez-Santoyo, A.
History
DepositionMar 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,71611
Polymers33,8872
Non-polymers8299
Water3,729207
1
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3125
Polymers16,9431
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4046
Polymers16,9431
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.438, 63.690, 66.287
Angle α, β, γ (deg.)90.00, 120.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lectin


Mass: 16943.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mytilus californianus (California mussel) / References: UniProt: A0A0P0E482
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium thiocyanate, 0.1 M Bis-Tris Propane pH 8.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 101 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 26332 / % possible obs: 95.06 % / Redundancy: 4.4 % / CC1/2: 0.85 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.04 / Net I/σ(I): 28.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2722)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMV

3wmv


Resolution: 1.788→35.088 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.36
RfactorNum. reflection% reflection
Rfree0.2249 1329 5.05 %
Rwork0.183 --
obs0.1851 26327 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.788→35.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 54 207 2651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012524
X-RAY DIFFRACTIONf_angle_d1.0483398
X-RAY DIFFRACTIONf_dihedral_angle_d5.5142076
X-RAY DIFFRACTIONf_chiral_restr0.063359
X-RAY DIFFRACTIONf_plane_restr0.007439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7883-1.85990.30751070.23842267X-RAY DIFFRACTION78
1.8599-1.94450.29211440.22442689X-RAY DIFFRACTION93
1.9445-2.0470.28491400.21172776X-RAY DIFFRACTION95
2.047-2.17530.26931590.20282787X-RAY DIFFRACTION96
2.1753-2.34320.24291550.1942874X-RAY DIFFRACTION98
2.3432-2.57890.24181640.2072870X-RAY DIFFRACTION99
2.5789-2.95190.24911410.19782882X-RAY DIFFRACTION98
2.9519-3.71850.20131520.17262927X-RAY DIFFRACTION99
3.7185-35.09430.17791670.14752926X-RAY DIFFRACTION98

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