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- PDB-8jea: Crystal structure of CGL1 from Crassostrea gigas, mannotriose-bou... -

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Basic information

Entry
Database: PDB / ID: 8jea
TitleCrystal structure of CGL1 from Crassostrea gigas, mannotriose-bound form (CGL1/Man(alpha)1-2Man(alpha)1-2Man)
ComponentsNatterin-3
KeywordsSUGAR BINDING PROTEIN / Crassostrea gigas / CGL1 / Mannotriose / Man3 / 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: 0.97 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)63,27914
Polymers61,7904
Non-polymers1,48810
Water14,682815
1
A: Natterin-3
D: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6998
Polymers30,8952
Non-polymers8046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-6 kcal/mol
Surface area11610 Å2
MethodPISA
2
B: Natterin-3
C: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5806
Polymers30,8952
Non-polymers6854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint1 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.734, 58.674, 108.410
Angle α, β, γ (deg.)90.000, 93.657, 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: 15447.538 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 , 3 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a6-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
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
#7: 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 , 4 types, 822 molecules

#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


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


Mass: 18.015 Da / Num. of mol.: 815 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate (pH 6.5), 20% 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: 0.97→39.771 Å / Num. obs: 292966 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.036 / Net I/σ(I): 28.6
Reflection shellResolution: 0.97→0.99 Å / Rmerge(I) obs: 1.021 / Num. unique obs: 14427 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.97→39.771 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.172 / Average fsc free: 0.9694 / Average fsc work: 0.9717 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.026
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1885 14810 5.056 %
Rwork0.1751 278118 -
all0.176 --
obs-292928 99.988 %
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: 11.064 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0 Å2-0.001 Å2
2--0.015 Å2-0 Å2
3----0.013 Å2
Refinement stepCycle: LAST / Resolution: 0.97→39.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 95 815 5270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124640
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164222
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.6526315
X-RAY DIFFRACTIONr_angle_other_deg0.9931.5679853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.245590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.098516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80210724
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.91510193
X-RAY DIFFRACTIONr_chiral_restr0.0990.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025221
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02908
X-RAY DIFFRACTIONr_nbd_refined0.2110.2649
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.23800
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22287
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1070.22333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2425
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2960.241
X-RAY DIFFRACTIONr_nbd_other0.2510.2164
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1190.2189
X-RAY DIFFRACTIONr_mcbond_it2.1421.0492303
X-RAY DIFFRACTIONr_mcbond_other2.1421.0492303
X-RAY DIFFRACTIONr_mcangle_it2.2211.582861
X-RAY DIFFRACTIONr_mcangle_other2.2211.5812862
X-RAY DIFFRACTIONr_scbond_it2.9281.3062337
X-RAY DIFFRACTIONr_scbond_other2.9291.3062338
X-RAY DIFFRACTIONr_scangle_it2.9311.8633439
X-RAY DIFFRACTIONr_scangle_other2.9311.8633440
X-RAY DIFFRACTIONr_lrange_it3.37438.2225361
X-RAY DIFFRACTIONr_lrange_other3.34137.6785316
X-RAY DIFFRACTIONr_rigid_bond_restr15.56238862
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
0.97-0.9950.29210950.287205210.288216290.9390.94199.93990.246
0.995-1.0220.26610750.266198800.266209550.9510.9511000.222
1.022-1.0520.2439870.245195220.245205100.960.95999.99510.203
1.052-1.0840.2479650.232188790.233198440.9590.9641000.191
1.084-1.120.2159350.214183330.214192680.9690.971000.177
1.12-1.1590.219050.198177560.199186610.9720.9741000.166
1.159-1.2030.219290.193171560.194180850.9720.9751000.164
1.203-1.2520.2028990.196163890.196172880.9740.9751000.166
1.252-1.3080.2098630.191157330.192165960.9710.9761000.166
1.308-1.3710.2068070.186151560.188159630.9740.9771000.164
1.371-1.4450.1868000.179142890.179150890.9770.981000.16
1.445-1.5330.1946990.169136230.17143220.9770.9821000.155
1.533-1.6390.1866630.162128030.163134670.9790.98399.99260.154
1.639-1.770.1836540.163119020.164125570.980.98499.9920.16
1.77-1.9380.1755910.159109450.16115380.9810.98599.98270.164
1.938-2.1660.1745630.15799150.158104790.9830.98599.99050.17
2.166-2.50.1695050.15987600.15992730.9820.98599.91370.178
2.5-3.0590.1854000.16374610.16478640.9790.98499.96190.192
3.059-4.3140.1593090.14957880.1560980.9860.98799.98360.186
4.314-39.7710.1671660.16233070.16234740.9850.98699.97120.208

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