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- PDB-5f8s: Crystal structure of a Crenomytilus grayanus lectin -

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Basic information

Entry
Database: PDB / ID: 5f8s
TitleCrystal structure of a Crenomytilus grayanus lectin
ComponentsGalNAc/Gal-specific lectin
KeywordsSUGAR BINDING PROTEIN / Lectin
Function / homologyTrefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / carbohydrate binding / Mainly Beta / Galactose-binding lectin
Function and homology information
Biological speciesCrenomytilus grayanus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.08 Å
AuthorsLiao, J.-H. / Huang, K.-F. / Tu, I.-F. / Lee, I.-M. / Wu, S.-H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council and Ministry of Science and TechnologyNSC 100-2113-M-001-022-MY3, NSC 102-2811-M-001-132, MOST 103-2113-M-001-029-MY3, MOST 103-2811-M-001-126, NSC 103-2923-M-001-006-MY3, NSC 100-2113-M-001-031-MY2, NSC 102-2113-M-001-017-MY2 Taiwan
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: A Multivalent Marine Lectin from Crenomytilus grayanus Possesses Anti-cancer Activity through Recognizing Globotriose Gb3
Authors: Liao, J.-H. / Chien, C.-T. / Wu, H.-Y. / Huang, K.-F. / Wang, I. / Ho, M.-R. / Tu, I.-F. / Lee, I.-M. / Li, W. / Shih, Y.-L. / Wu, C.-Y. / Lukyanov, P.A. / Hsu, S.D. / Wu, S.-H.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: GalNAc/Gal-specific lectin
B: GalNAc/Gal-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,50110
Polymers35,7652
Non-polymers7378
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-10 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.841, 71.062, 93.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GalNAc/Gal-specific lectin


Mass: 17882.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crenomytilus grayanus (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: H2FH31
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M imidazole malate, 25%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.08→30 Å / Num. obs: 149358 / % possible obs: 98.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 23.9
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.08→30 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.733 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13131 7345 4.9 %RANDOM
Rwork0.11367 ---
obs0.11453 141923 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.412 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0 Å2
2--0.39 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.08→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 48 555 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192529
X-RAY DIFFRACTIONr_bond_other_d0.0040.022359
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.933412
X-RAY DIFFRACTIONr_angle_other_deg1.0683.0075441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5685302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63123.968126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00515404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3111510
X-RAY DIFFRACTIONr_chiral_restr0.2320.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212873
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02629
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8560.7561202
X-RAY DIFFRACTIONr_mcbond_other0.8150.7551201
X-RAY DIFFRACTIONr_mcangle_it0.9831.141503
X-RAY DIFFRACTIONr_mcangle_other1.0131.1411504
X-RAY DIFFRACTIONr_scbond_it2.2650.9491327
X-RAY DIFFRACTIONr_scbond_other2.2680.951328
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8561.3491909
X-RAY DIFFRACTIONr_long_range_B_refined5.0599.7333307
X-RAY DIFFRACTIONr_long_range_B_other3.9557.4842947
X-RAY DIFFRACTIONr_rigid_bond_restr1.39434888
X-RAY DIFFRACTIONr_sphericity_free39.2255160
X-RAY DIFFRACTIONr_sphericity_bonded9.66355212
LS refinement shellResolution: 1.08→1.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 565 -
Rwork0.231 10341 -
obs--98.3 %

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