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- PDB-7yl5: Cell surface protein YwfG protein complexed with mannose -

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Basic information

Entry
Database: PDB / ID: 7yl5
TitleCell surface protein YwfG protein complexed with mannose
ComponentsGRAM_POS_ANCHORING domain-containing protein
KeywordsCELL ADHESION / mannose-binding
Function / homology
Function and homology information


extracellular region / metal ion binding / membrane
Similarity search - Function
Mucin binding domain / Mucin binding domain / : / MucBP domain / MucBP domain / Legume lectin beta-barrel domain / Mub B2-like domain / Muc B2-like domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...Mucin binding domain / Mucin binding domain / : / MucBP domain / MucBP domain / Legume lectin beta-barrel domain / Mub B2-like domain / Muc B2-like domain / 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
alpha-D-mannopyranose / 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: 3 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)111,10932
Polymers108,0872
Non-polymers3,02230
Water59433
1
A: GRAM_POS_ANCHORING domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,12812
Polymers54,0441
Non-polymers1,08511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GRAM_POS_ANCHORING domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,98120
Polymers54,0441
Non-polymers1,93719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.312, 273.164, 322.789
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / 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
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4.42 Å3/Da / Density % sol: 72.15 %
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: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.71 Å / Num. obs: 39549 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.042 / Rrim(I) all: 0.151 / Net I/σ(I): 16
Reflection shellResolution: 3→3.16 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.053 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5675 / CC1/2: 0.806 / Rpim(I) all: 0.304 / Rrim(I) all: 1.097 / % possible all: 100

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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: 3→45.569 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.876 / SU B: 20.453 / SU ML: 0.344 / Cross valid method: FREE R-VALUE / ESU R: 0.542 / ESU R Free: 0.38
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2955 1964 4.982 %
Rwork0.2271 37457 -
all0.23 --
obs-39421 99.628 %
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: 79.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.021 Å2-0 Å2-0 Å2
2---0.086 Å20 Å2
3---0.065 Å2
Refinement stepCycle: LAST / Resolution: 3→45.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6446 0 163 33 6642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0136705
X-RAY DIFFRACTIONr_bond_other_d0.0020.0185886
X-RAY DIFFRACTIONr_angle_refined_deg2.2791.6579140
X-RAY DIFFRACTIONr_angle_other_deg1.4371.5913551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6955857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.43425.633316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.52315982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1221510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027858
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021562
X-RAY DIFFRACTIONr_nbd_refined0.220.21168
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.25492
X-RAY DIFFRACTIONr_nbtor_refined0.1880.23030
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.23440
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2183
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.25
X-RAY DIFFRACTIONr_metal_ion_refined0.3850.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.210
X-RAY DIFFRACTIONr_nbd_other0.260.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.26
X-RAY DIFFRACTIONr_mcbond_it11.4918.4093437
X-RAY DIFFRACTIONr_mcbond_other11.4848.4073436
X-RAY DIFFRACTIONr_mcangle_it15.2512.6044291
X-RAY DIFFRACTIONr_mcangle_other15.2512.6064292
X-RAY DIFFRACTIONr_scbond_it12.6258.7853268
X-RAY DIFFRACTIONr_scbond_other11.9728.7233204
X-RAY DIFFRACTIONr_scangle_it16.88213.0084849
X-RAY DIFFRACTIONr_scangle_other16.28612.9384754
X-RAY DIFFRACTIONr_lrange_it18.6394.9556747
X-RAY DIFFRACTIONr_lrange_other18.64494.9566747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0780.3921290.3652804X-RAY DIFFRACTION100
3.078-3.1620.41400.3282602X-RAY DIFFRACTION100
3.162-3.2540.3761480.3152590X-RAY DIFFRACTION99.9635
3.254-3.3540.341160.2832549X-RAY DIFFRACTION99.9625
3.354-3.4640.321290.2762390X-RAY DIFFRACTION99.6834
3.464-3.5860.3411200.2452411X-RAY DIFFRACTION99.9605
3.586-3.7210.3571180.2442242X-RAY DIFFRACTION99.7886
3.721-3.8730.2951180.2252220X-RAY DIFFRACTION99.659
3.873-4.0450.2641080.2172089X-RAY DIFFRACTION99.1874
4.045-4.2420.321050.2182035X-RAY DIFFRACTION99.2119
4.242-4.4720.2671120.1911879X-RAY DIFFRACTION98.711
4.472-4.7430.278950.1741841X-RAY DIFFRACTION99.1803
4.743-5.070.195840.1621713X-RAY DIFFRACTION99.612
5.07-5.4760.236830.1731645X-RAY DIFFRACTION99.5965
5.476-5.9980.279860.1891478X-RAY DIFFRACTION99.6178
5.998-6.7060.271740.1941362X-RAY DIFFRACTION99.9304
6.706-7.7420.251540.2011227X-RAY DIFFRACTION99.8441
7.742-9.4780.291550.2021049X-RAY DIFFRACTION99.729
9.478-13.390.291540.24837X-RAY DIFFRACTION99.8879
13.39-45.5690.319360.317494X-RAY DIFFRACTION96.5392

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