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- PDB-9m00: Crystal Structure of the Basal pilin EbpB from Enterococcus faeca... -

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Basic information

Entry
Database: PDB / ID: 9m00
TitleCrystal Structure of the Basal pilin EbpB from Enterococcus faecalis with a partially disordered N-terminal domain.
ComponentsEndocarditis and biofilm-associated pilus minor subunit EbpB.
KeywordsCELL ADHESION / Basal Pilin / Isopeptide bond / Ebp pili / CAUTI / Enterococcus faecalis
Biological speciesEnterococcus faecalis OG1RF (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionFeb 23, 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.


Theoretical massNumber of molelcules
Total (without water)97,3692
Polymers97,3692
Non-polymers00
Water3,225179
1
B: Endocarditis and biofilm-associated pilus minor subunit EbpB.


Theoretical massNumber of molelcules
Total (without water)48,6841
Polymers48,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Endocarditis and biofilm-associated pilus minor subunit EbpB.


Theoretical massNumber of molelcules
Total (without water)48,6841
Polymers48,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.300, 48.080, 127.010
Angle α, β, γ (deg.)96.44, 98.04, 90.12
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 48684.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-domain form of Basal pilin EbpB is partially disordered. 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 100mM SPG buffer pH 9, 25% (w/v) PEG 1500

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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: 2.7→43.06 Å / Num. obs: 22438 / % possible obs: 89.4 % / Redundancy: 2.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.079 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.76 Å / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1122 / CC1/2: 0.921 / Rpim(I) all: 0.193

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→43.06 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.809 / SU B: 25.517 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 1.344 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27918 1183 5.3 %RANDOM
Rwork0.23986 ---
obs0.24193 21254 89.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.425 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20.57 Å20.1 Å2
2---0.43 Å20.38 Å2
3---1.56 Å2
Refinement stepCycle: 1 / Resolution: 2.7→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4809 0 0 179 4988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124884
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164568
X-RAY DIFFRACTIONr_angle_refined_deg1.51.8446613
X-RAY DIFFRACTIONr_angle_other_deg0.4951.77310512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6055620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.283510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74610805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021032
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_it0.1160.3752534
X-RAY DIFFRACTIONr_mcbond_other0.1160.3752534
X-RAY DIFFRACTIONr_mcangle_it0.2160.673136
X-RAY DIFFRACTIONr_mcangle_other0.2160.673137
X-RAY DIFFRACTIONr_scbond_it0.0830.3692350
X-RAY DIFFRACTIONr_scbond_other0.0830.3692351
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.1610.6813478
X-RAY DIFFRACTIONr_long_range_B_refined1.0294.4319473
X-RAY DIFFRACTIONr_long_range_B_other0.9264.4119413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 60 -
Rwork0.271 1265 -
obs--72.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.33130.5539-2.65480.4564-0.08332.4376-0.0501-0.36940.02040.09070.1250.21780.1337-0.0087-0.07490.4449-0.00880.08180.61290.01020.3098-19.364.48350.708
22.4335-0.4484-0.91831.1660.07771.31910.0213-0.17350.04640.1559-0.015-0.04250.0152-0.0125-0.00620.178-0.0280.00180.1095-0.02440.00758.35211.81325.187
33.9629-0.6002-1.21732.0888-1.05442.2456-0.04590.23860.2413-0.11620.0212-0.0549-0.10210.01510.02460.1425-0.04740.00120.0706-0.01850.070833.20710.537-3.459
43.0963-1.6332-2.21920.95921.19981.72180.07290.3620.3173-0.10570.0492-0.30520.1331-0.0576-0.12210.5751-0.04730.15040.6643-0.06860.420140.227.139-30.814
52.01530.456-0.78521.3623-0.22580.86550.03540.12010.0088-0.1406-0.02290.0018-0.0730.0371-0.01240.1913-0.0188-0.00590.12620.00110.016113.88935.86-4.804
63.35820.2175-1.28312.76131.0041.97070.0193-0.23030.22420.08310.00090.0531-0.1639-0.0558-0.02020.11910.004-0.00590.073-0.00420.0415-10.98334.63623.758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 186
2X-RAY DIFFRACTION2A187 - 319
3X-RAY DIFFRACTION3A320 - 434
4X-RAY DIFFRACTION4B36 - 186
5X-RAY DIFFRACTION5B187 - 319
6X-RAY DIFFRACTION6B320 - 434

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