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- PDB-8jeb: Crystal structure of CGL1 from Crassostrea gigas, mannotetraose-b... -

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Basic information

Entry
Database: PDB / ID: 8jeb
TitleCrystal structure of CGL1 from Crassostrea gigas, mannotetraose-bound form (CGL1/Man(alpha)1-2Man(alpha)1-2Man(alpha)1-6Man)
ComponentsNatterin-3
KeywordsSUGAR BINDING PROTEIN / Crassostrea gigas / CGL1 / Mannotetraose / Man4 / complex structure
Function / homologyDM9 repeat / DM9 repeat / Repeats found in Drosophila proteins. / metal ion binding / ACETIC ACID / Natterin-3
Function and homology information
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
B: Natterin-3
A: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,68616
Polymers30,8952
Non-polymers1,79114
Water5,549308
1
B: Natterin-3
A: Natterin-3
hetero molecules

B: Natterin-3
A: Natterin-3
hetero molecules

B: Natterin-3
A: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,05848
Polymers92,6856
Non-polymers5,37342
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Buried area3200 Å2
ΔGint-25 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.400, 82.495, 44.201
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Natterin-3


Mass: 15447.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Crassostrea gigas (Pacific oyster) / References: UniProt: K1QRB6

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Sugars , 2 types, 4 molecules

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


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(6+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.: 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
[][D-1-deoxy-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 318 molecules

#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C2H4O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
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: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→44.201 Å / Num. obs: 68918 / % possible obs: 99.2 % / Redundancy: 12.5 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.9
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.747 / Num. unique obs: 3007 / CC1/2: 0.837

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→44.201 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.167 / WRfactor Rwork: 0.151 / SU B: 0.786 / SU ML: 0.032 / Average fsc free: 0.9718 / Average fsc work: 0.9774 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.046
Details: The chirality error is due to by the orientations and interactions between residues and ligands in the protein-ligand complex structure. Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1745 3467 5.035 %
Rwork0.1564 65391 -
all0.157 --
obs-68858 99.183 %
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: 14.566 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0 Å2-0 Å2
2---0.002 Å20 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 1.3→44.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 115 308 2603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122341
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162163
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6613177
X-RAY DIFFRACTIONr_angle_other_deg0.5791.5725006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3985280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.19258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65410352
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.6811094
X-RAY DIFFRACTIONr_chiral_restr0.3130.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022614
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
X-RAY DIFFRACTIONr_nbd_refined0.2560.2363
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.21936
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21167
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21198
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2168
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0450.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.7350.218
X-RAY DIFFRACTIONr_nbd_other0.1940.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.226
X-RAY DIFFRACTIONr_mcbond_it1.0921.4111137
X-RAY DIFFRACTIONr_mcbond_other1.0571.4061132
X-RAY DIFFRACTIONr_mcangle_it1.4832.5281408
X-RAY DIFFRACTIONr_mcangle_other1.4832.5281409
X-RAY DIFFRACTIONr_scbond_it3.0051.6791204
X-RAY DIFFRACTIONr_scbond_other3.0041.681205
X-RAY DIFFRACTIONr_scangle_it4.2862.9611769
X-RAY DIFFRACTIONr_scangle_other4.2852.9611770
X-RAY DIFFRACTIONr_lrange_it4.86719.3262600
X-RAY DIFFRACTIONr_lrange_other4.81217.9242544
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
1.3-1.3340.2842230.26943500.2750280.9350.94190.95070.213
1.334-1.370.2742470.24845730.24949280.9440.95397.80840.189
1.37-1.410.2332450.2145470.21147920.9630.9681000.161
1.41-1.4530.2342390.244260.20246660.9570.97299.97860.158
1.453-1.5010.2122270.18843530.18945800.9680.9751000.148
1.501-1.5540.1992020.17241740.17343780.9730.9899.95430.136
1.554-1.6120.1862190.15840240.15942430.9780.9841000.13
1.612-1.6780.191750.15539010.15740760.9770.9841000.129
1.678-1.7520.1981840.14737500.14939340.9770.9861000.127
1.752-1.8380.1582170.14735740.14837910.9830.9871000.128
1.838-1.9370.1691790.14833680.14935470.9830.9871000.135
1.937-2.0540.1671850.14732160.14834010.9840.9871000.137
2.054-2.1960.1622070.14330090.14432160.9860.9881000.136
2.196-2.3710.1511690.14228130.14329820.9850.9881000.142
2.371-2.5970.1921390.15426470.15627860.9780.9851000.155
2.597-2.9020.181130.1623710.16124840.9790.9841000.168
2.902-3.3480.168930.15421610.15522540.9830.9851000.169
3.348-4.0950.131730.13318320.13319050.9910.991000.151
4.095-5.7670.129760.12914440.12915200.9920.9911000.154
5.767-44.2010.216550.1978580.1989130.9780.9771000.224

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