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- PDB-9lr7: Crystal Structure of the Basal pilin EbpB from Enterococcus faecalis. -

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Basic information

Entry
Database: PDB / ID: 9lr7
TitleCrystal Structure of the Basal pilin EbpB from Enterococcus faecalis.
ComponentsEndocarditis and biofilm-associated pilus minor subunit EbpB
KeywordsCELL ADHESION / Basal Pilin / Isopeptide bond / Ebp pili / CAUTI / Enterococcus faecalis
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesEnterococcus faecalis OG1RF (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSharma, V. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR44816/MED/29/1598/2022 India
CitationJournal: Febs J. / Year: 2025
Title: Structural basis of Ebp pilus shaft formation and anchoring in vancomycin-resistant Enterococci.
Authors: Sharma, V. / Krishnan, V.
History
DepositionJan 30, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Endocarditis and biofilm-associated pilus minor subunit EbpB
A: Endocarditis and biofilm-associated pilus minor subunit EbpB
C: Endocarditis and biofilm-associated pilus minor subunit EbpB
D: Endocarditis and biofilm-associated pilus minor subunit EbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,64826
Polymers194,7374
Non-polymers91122
Water3,009167
1
B: Endocarditis and biofilm-associated pilus minor subunit EbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9337
Polymers48,6841
Non-polymers2496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-24 kcal/mol
Surface area21110 Å2
MethodPISA
2
A: Endocarditis and biofilm-associated pilus minor subunit EbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9337
Polymers48,6841
Non-polymers2496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-25 kcal/mol
Surface area19860 Å2
MethodPISA
3
C: Endocarditis and biofilm-associated pilus minor subunit EbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8716
Polymers48,6841
Non-polymers1875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area18760 Å2
MethodPISA
4
D: Endocarditis and biofilm-associated pilus minor subunit EbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9106
Polymers48,6841
Non-polymers2265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.307, 158.415, 88.221
Angle α, β, γ (deg.)90.00, 92.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endocarditis and biofilm-associated pilus minor subunit EbpB


Mass: 48684.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A full-length recombinant three domains Basal pilin EbpB from Enterococcus faecalis. Sequence refers to database WP_002413529.1.
Source: (gene. exp.) Enterococcus faecalis OG1RF (bacteria) / Strain: OG1RF / Gene: ebpB, GTI81_12235 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 200mM Ammonium sulfate, 100mM Sodium acetate HCl, pH 4.6, 25% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.43→77.15 Å / Num. obs: 74323 / % possible obs: 93.5 % / Redundancy: 3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.067 / Net I/σ(I): 7.4
Reflection shellResolution: 2.43→2.52 Å / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3716 / CC1/2: 0.634 / Rpim(I) all: 0.41 / % possible all: 75.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→77.15 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.879 / SU B: 27.054 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3511 4.7 %RANDOM
Rwork0.21872 ---
obs0.22042 70812 82.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.968 Å2
Baniso -1Baniso -2Baniso -3
1--9.87 Å2-0 Å2-1.33 Å2
2--5.82 Å2-0 Å2
3---4.13 Å2
Refinement stepCycle: 1 / Resolution: 2.43→77.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11674 0 47 167 11888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01212005
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611112
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.83616265
X-RAY DIFFRACTIONr_angle_other_deg0.4811.75225542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76151532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.123534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.109101917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.21910
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022557
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6653.1016170
X-RAY DIFFRACTIONr_mcbond_other5.6633.1016170
X-RAY DIFFRACTIONr_mcangle_it9.0235.5677688
X-RAY DIFFRACTIONr_mcangle_other9.0225.5677689
X-RAY DIFFRACTIONr_scbond_it5.8873.1615835
X-RAY DIFFRACTIONr_scbond_other5.8723.165811
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.1025.7758554
X-RAY DIFFRACTIONr_long_range_B_refined19.89937.5447727
X-RAY DIFFRACTIONr_long_range_B_other19.04137.5347703
X-RAY DIFFRACTIONr_rigid_bond_restr5.561323117
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 123 -
Rwork0.312 2097 -
obs--33.54 %

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