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- PDB-7yl6: Cell surface protein YwfG protein complexed with alpha-1,2-mannobiose -

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Basic information

Entry
Database: PDB / ID: 7yl6
TitleCell surface protein YwfG protein complexed with alpha-1,2-mannobiose
ComponentsGRAM_POS_ANCHORING domain-containing protein
KeywordsCELL ADHESION / mannose-binding
Function / homology
Function and homology information


extracellular region / membrane / metal ion binding
Similarity search - Function
Mucin binding domain / Mucin binding domain / MucBP domain / MucBP domain / Mub B2-like domain / Muc B2-like domain / Bacterial lectin / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
2alpha-alpha-mannobiose / Gram-positive cocci surface proteins LPxTG domain-containing protein
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.95 Å
AuthorsTsuchiya, W. / Fujimoto, Z. / Suzuki, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos One / Year: 2023
Title: Cell-surface protein YwfG of Lactococcus lactis binds to alpha-1,2-linked mannose.
Authors: Tsuchiya, W. / Fujimoto, Z. / Inagaki, N. / Nakagawa, H. / Tanaka, M. / Kimoto-Nira, H. / Yamazaki, T. / Suzuki, C.
History
DepositionJul 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRAM_POS_ANCHORING domain-containing protein
B: GRAM_POS_ANCHORING domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,81216
Polymers108,0872
Non-polymers1,72514
Water73941
1
A: GRAM_POS_ANCHORING domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9068
Polymers54,0441
Non-polymers8637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22790 Å2
MethodPISA
2
B: GRAM_POS_ANCHORING domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9068
Polymers54,0441
Non-polymers8637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.454, 276.634, 321.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein GRAM_POS_ANCHORING domain-containing protein


Mass: 54043.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: llmg_2465, O9U_11750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S6FKX6
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
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: 4.37 Å3/Da / Density % sol: 71.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate (pH 5.0-5.6), 1.3 M Li2SO4, 2% (w/v) polyethylene glycol 3350
PH range: 5.0-5.6

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→43.06 Å / Num. obs: 42029 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.996 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.058 / Rrim(I) all: 0.211 / Net I/σ(I): 14
Reflection shellResolution: 2.95→3.11 Å / Rmerge(I) obs: 1.187 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6070 / CC1/2: 0.774 / Rpim(I) all: 0.329 / Rrim(I) all: 1.232

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7YL4

7yl4


Resolution: 2.95→41.511 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.879 / SU B: 17.595 / SU ML: 0.293 / Cross valid method: FREE R-VALUE / ESU R: 0.452 / ESU R Free: 0.33
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2684 2151 5.119 %
Rwork0.2114 39872 -
all0.214 --
obs-42023 99.888 %
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: 65.208 Å2
Baniso -1Baniso -2Baniso -3
1--1.638 Å20 Å2-0 Å2
2--1.913 Å20 Å2
3----0.276 Å2
Refinement stepCycle: LAST / Resolution: 2.95→41.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 98 41 6673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136748
X-RAY DIFFRACTIONr_bond_other_d0.0020.0185965
X-RAY DIFFRACTIONr_angle_refined_deg2.0331.669187
X-RAY DIFFRACTIONr_angle_other_deg1.4061.59213731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.92725.556324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.63115995
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7241511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027971
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021591
X-RAY DIFFRACTIONr_nbd_refined0.2120.21071
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.25384
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23103
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.23494
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0910.23
X-RAY DIFFRACTIONr_metal_ion_refined0.3580.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.216
X-RAY DIFFRACTIONr_nbd_other0.210.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0450.23
X-RAY DIFFRACTIONr_mcbond_it7.5466.8363477
X-RAY DIFFRACTIONr_mcbond_other7.5396.8343476
X-RAY DIFFRACTIONr_mcangle_it10.73810.244341
X-RAY DIFFRACTIONr_mcangle_other10.73810.2424342
X-RAY DIFFRACTIONr_scbond_it8.4767.2093271
X-RAY DIFFRACTIONr_scbond_other8.3227.193256
X-RAY DIFFRACTIONr_scangle_it12.23810.6814846
X-RAY DIFFRACTIONr_scangle_other12.04610.6544823
X-RAY DIFFRACTIONr_lrange_it13.98776.6026765
X-RAY DIFFRACTIONr_lrange_other13.96276.6016764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.0270.3871610.3612867X-RAY DIFFRACTION100
3.027-3.110.3931710.3332870X-RAY DIFFRACTION100
3.11-3.20.3641540.3032675X-RAY DIFFRACTION100
3.2-3.2980.3541410.292717X-RAY DIFFRACTION100
3.298-3.4060.3211260.2712602X-RAY DIFFRACTION100
3.406-3.5260.3141480.2412475X-RAY DIFFRACTION99.9238
3.526-3.6590.3011250.2262466X-RAY DIFFRACTION99.9614
3.659-3.8080.2481120.2132325X-RAY DIFFRACTION100
3.808-3.9770.2591200.2082293X-RAY DIFFRACTION100
3.977-4.1720.2311220.1862111X-RAY DIFFRACTION100
4.172-4.3970.2281110.182085X-RAY DIFFRACTION100
4.397-4.6640.2371010.1741938X-RAY DIFFRACTION99.951
4.664-4.9860.206930.1531855X-RAY DIFFRACTION99.9487
4.986-5.3850.186920.1581740X-RAY DIFFRACTION99.9454
5.385-5.8980.232980.1721567X-RAY DIFFRACTION100
5.898-6.5940.269760.1661446X-RAY DIFFRACTION99.9343
6.594-7.6130.238720.1641315X-RAY DIFFRACTION100
7.613-9.320.229560.1661120X-RAY DIFFRACTION100
9.32-13.1680.23430.189892X-RAY DIFFRACTION100
13.168-41.5110.359290.275513X-RAY DIFFRACTION93.1272

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