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- PDB-8je9: Crystal structure of CGL1 from Crassostrea gigas, mannobiose-boun... -

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Basic information

Entry
Database: PDB / ID: 8je9
TitleCrystal structure of CGL1 from Crassostrea gigas, mannobiose-bound form (CGL1/Man(alpha)1-2Man)
ComponentsNatterin-3
KeywordsSUGAR BINDING PROTEIN / complex structure
Function / homologyDM9 repeat / DM9 repeat / Repeats found in Drosophila proteins. / metal ion binding / ACETIC ACID / CACODYLATE ION / alpha-D-mannopyranose / Natterin-3
Function and homology information
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsUnno, H. / Hatakeyama, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other government Japan
CitationJournal: J.Biochem. / Year: 2023
Title: Mannose oligosaccharide recognition of CGL1, a mannose-specific lectin containing DM9 motifs from Crassostrea gigas, revealed by X-ray crystallographic analysis.
Authors: Hatakeyama, T. / Masuda, K. / Kudo, M. / Tanaka, K. / Takeuchi, A. / Unno, H.
History
DepositionMay 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Natterin-3
B: Natterin-3
C: Natterin-3
D: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49711
Polymers62,3154
Non-polymers1,1827
Water14,448802
1
A: Natterin-3
D: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8776
Polymers31,1572
Non-polymers7194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-1 kcal/mol
Surface area11570 Å2
MethodPISA
2
B: Natterin-3
C: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6205
Polymers31,1572
Non-polymers4623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-2 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.749, 58.701, 108.405
Angle α, β, γ (deg.)90.000, 93.701, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Natterin-3


Mass: 15578.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Crassostrea gigas (Pacific oyster) / References: UniProt: K1QRB6

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 806 molecules

#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate (pH 6.5), 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→39.8 Å / Num. obs: 229413 / % possible obs: 85.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.6
Reflection shellResolution: 1→1.02 Å / Num. unique obs: 4020 / CC1/2: 0.872

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→39.778 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.192 / Average fsc free: 0.9723 / Average fsc work: 0.976 / Cross valid method: FREE R-VALUE / ESU R: 0.033 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1869 11557 5.038 %
Rwork0.1744 217829 -
all0.175 --
obs-229386 85.767 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0 Å20.013 Å2
2--0.007 Å2-0 Å2
3----0.008 Å2
Refinement stepCycle: LAST / Resolution: 1→39.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 75 802 5237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124602
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164183
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.6516255
X-RAY DIFFRACTIONr_angle_other_deg1.0171.5679758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3125582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.519516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51710721
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.98410192
X-RAY DIFFRACTIONr_chiral_restr0.1070.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025181
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02903
X-RAY DIFFRACTIONr_nbd_refined0.2050.2649
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.23764
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22280
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1060.22362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2416
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3630.239
X-RAY DIFFRACTIONr_nbd_other0.2840.2168
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.2168
X-RAY DIFFRACTIONr_mcbond_it1.0951.0532293
X-RAY DIFFRACTIONr_mcbond_other1.0951.0532293
X-RAY DIFFRACTIONr_mcangle_it1.4661.592849
X-RAY DIFFRACTIONr_mcangle_other1.4661.592850
X-RAY DIFFRACTIONr_scbond_it1.2311.2692309
X-RAY DIFFRACTIONr_scbond_other1.2331.2692310
X-RAY DIFFRACTIONr_scangle_it1.6151.8233395
X-RAY DIFFRACTIONr_scangle_other1.6151.8233396
X-RAY DIFFRACTIONr_lrange_it2.76735.8575299
X-RAY DIFFRACTIONr_lrange_other2.76735.8565299
X-RAY DIFFRACTIONr_rigid_bond_restr14.95638785
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1-1.0260.2773680.27963100.279197660.9430.94633.78530.25
1.026-1.0540.2754900.25695520.257191370.9450.95752.47430.228
1.054-1.0850.2356880.235137740.235186820.9640.96577.41140.211
1.085-1.1180.2267410.215156360.216181240.9660.9790.36080.194
1.118-1.1550.2088230.204152630.204176070.9730.97391.36140.188
1.155-1.1960.2187800.199148890.2170220.970.97592.05150.186
1.196-1.2410.2177560.197144960.198164800.970.97592.54850.184
1.241-1.2910.2117480.198139540.199157700.9730.97593.22760.188
1.291-1.3490.2146810.194135300.195151430.9710.97693.84530.187
1.349-1.4140.2057020.184130590.185145670.9730.97894.46690.181
1.414-1.4910.27060.174123450.175137530.9750.98194.89570.174
1.491-1.5810.1816110.167119440.168131220.9810.98395.6790.174
1.581-1.690.1766360.163111480.164122620.9810.98496.10180.175
1.69-1.8250.1765890.157105070.158114690.9810.98596.74780.177
1.825-1.9990.1745570.16296960.163105510.9820.98497.17560.189
1.999-2.2340.1964810.16188530.16395520.9780.98497.71780.197
2.234-2.5780.1744030.16578960.16584460.9820.98498.25950.208
2.578-3.1550.1773460.16767280.16871620.9820.98398.77130.22
3.155-4.4470.1523020.1552530.15156060.9870.98799.09030.205
4.447-39.7780.1731490.17729960.17731640.9760.98499.39950.254

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