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- PDB-3wmu: The structure of an anti-cancer lectin mytilec apo-form from the ... -

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Basic information

Entry
Database: PDB / ID: 3wmu
TitleThe structure of an anti-cancer lectin mytilec apo-form from the mussel Mytilus galloprovincialis
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE
Function / homologygalactose binding / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / killing of cells of another organism / Mainly Beta / Alpha-D-galactose-binding lectin
Function and homology information
Biological speciesMytilus galloprovincialis (Mediterranean mussel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsTerada, D. / Kawai, F. / Noguchi, H. / Unzai, S. / Park, S.-Y. / Ozeki, Y. / Tame, J.R.H.
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of MytiLec, a galactose-binding lectin from the mussel Mytilus galloprovincialis with cytotoxicity against certain cancer cell types
Authors: Terada, D. / Kawai, F. / Noguchi, H. / Unzai, S. / Hasan, I. / Fujii, Y. / Park, S.-Y. / Ozeki, Y. / Tame, J.R.H.
History
DepositionNov 27, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9448
Polymers34,3912
Non-polymers5536
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-8 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.725, 41.507, 68.831
Angle α, β, γ (deg.)90.00, 108.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lectin / / MytiLec


Mass: 17195.615 Da / Num. of mol.: 2 / Mutation: T1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mytilus galloprovincialis (Mediterranean mussel)
Production host: Escherichia coli (E. coli) / References: UniProt: B3EWR1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodiumu acetate, HEPES, Glycerol, PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 24, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 120340 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.1→1.12 Å / Rmerge(I) obs: 0.298 / % possible all: 89.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→27.48 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.857 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16277 6025 5 %RANDOM
Rwork0.137 ---
obs0.13827 114309 95.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å20.29 Å2
2---0.91 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.1→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 36 341 2793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192547
X-RAY DIFFRACTIONr_bond_other_d0.0020.022429
X-RAY DIFFRACTIONr_angle_refined_deg2.2281.9413434
X-RAY DIFFRACTIONr_angle_other_deg2.10735614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5585312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30323.782119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29315431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2241510
X-RAY DIFFRACTIONr_chiral_restr0.1510.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212855
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02611
X-RAY DIFFRACTIONr_rigid_bond_restr17.26834976
X-RAY DIFFRACTIONr_sphericity_free27.5025104
X-RAY DIFFRACTIONr_sphericity_bonded9.41155142
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 430 -
Rwork0.244 7795 -
obs--88.93 %

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