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- PDB-7yl4: Cell surface protein YwfG protein (apo form) -

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Basic information

Entry
Database: PDB / ID: 7yl4
TitleCell surface protein YwfG protein (apo form)
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 / Mub B2-like domain / Muc B2-like domain / Legume lectin beta-barrel 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
Gram-positive cocci surface proteins LPxTG domain-containing protein
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)109,51218
Polymers108,0872
Non-polymers1,42516
Water1,33374
1
A: GRAM_POS_ANCHORING domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6608
Polymers54,0441
Non-polymers6167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22710 Å2
MethodPISA
2
B: GRAM_POS_ANCHORING domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,85210
Polymers54,0441
Non-polymers8099
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-17 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.219, 272.930, 320.332
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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 6M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.6 Å / Num. obs: 66894 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.026 / Rrim(I) all: 0.096 / Net I/σ(I): 21.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 9601 / CC1/2: 0.871 / Rpim(I) all: 0.229 / Rrim(I) all: 0.841 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m01

4m01


Resolution: 2.5→45.53 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.23 / SU B: 11.108 / SU ML: 0.23 / Average fsc free: 0.8199 / Average fsc work: 0.8372 / Cross valid method: FREE R-VALUE / ESU R: 0.265 / ESU R Free: 0.23
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2796 3224 4.82 %
Rwork0.2455 63669 -
all0.247 --
obs-66893 99.969 %
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: 65.081 Å2
Baniso -1Baniso -2Baniso -3
1--5.041 Å20 Å2-0 Å2
2--4.543 Å20 Å2
3---0.499 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6527 0 72 74 6673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136709
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185927
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.659137
X-RAY DIFFRACTIONr_angle_other_deg1.3451.58413635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0955866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.66525.556324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.11415994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2351511
X-RAY DIFFRACTIONr_chiral_restr0.0650.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027964
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021590
X-RAY DIFFRACTIONr_nbd_refined0.2020.21059
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.25407
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23037
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.23370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2192
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0650.23
X-RAY DIFFRACTIONr_metal_ion_refined0.2740.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.224
X-RAY DIFFRACTIONr_nbd_other0.2310.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.26
X-RAY DIFFRACTIONr_mcbond_it7.3226.9133473
X-RAY DIFFRACTIONr_mcbond_other7.3236.9113472
X-RAY DIFFRACTIONr_mcangle_it10.37310.3424336
X-RAY DIFFRACTIONr_mcangle_other10.37310.3444337
X-RAY DIFFRACTIONr_scbond_it7.477.1713236
X-RAY DIFFRACTIONr_scbond_other7.3527.1413205
X-RAY DIFFRACTIONr_scangle_it10.84610.6724801
X-RAY DIFFRACTIONr_scangle_other10.71910.6284754
X-RAY DIFFRACTIONr_lrange_it13.36576.8526730
X-RAY DIFFRACTIONr_lrange_other13.35976.8786725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.3952350.3854664X-RAY DIFFRACTION100
2.565-2.6350.3772150.364487X-RAY DIFFRACTION100
2.635-2.7120.3852210.344462X-RAY DIFFRACTION100
2.712-2.7950.3662240.3124197X-RAY DIFFRACTION100
2.795-2.8870.3192340.2994210X-RAY DIFFRACTION100
2.887-2.9880.322060.2913934X-RAY DIFFRACTION99.9759
2.988-3.1010.3052200.2793919X-RAY DIFFRACTION100
3.101-3.2270.341850.2723690X-RAY DIFFRACTION100
3.227-3.3710.31910.2663637X-RAY DIFFRACTION100
3.371-3.5350.2791720.263414X-RAY DIFFRACTION99.9721
3.535-3.7260.2851620.2553287X-RAY DIFFRACTION100
3.726-3.9520.261390.2353164X-RAY DIFFRACTION99.9697
3.952-4.2250.2631630.2252904X-RAY DIFFRACTION100
4.225-4.5640.2561210.2182738X-RAY DIFFRACTION100
4.564-4.9990.2571310.2072556X-RAY DIFFRACTION100
4.999-5.5890.2421000.1982327X-RAY DIFFRACTION100
5.589-6.4520.251070.2152065X-RAY DIFFRACTION100
6.452-7.9010.236900.191763X-RAY DIFFRACTION100
7.901-11.1650.171670.1721419X-RAY DIFFRACTION100
11.165-45.530.248410.251832X-RAY DIFFRACTION97.9798

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