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- PDB-9llw: Crystal Structure of N-terminal flexible domain of the Shaft pili... -

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Basic information

Entry
Database: PDB / ID: 9llw
TitleCrystal Structure of N-terminal flexible domain of the Shaft pilin EbpC from Enterococcus faecalis.
ComponentsIsopeptide-forming domain-containing fimbrial protein
KeywordsCELL ADHESION / Shaft Pilin / Isopeptide bond / Ebp pili / CAUTI / Pathogenic Bacteria.
Biological speciesEnterococcus faecalis OG1RF (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 17, 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
A: Isopeptide-forming domain-containing fimbrial protein


Theoretical massNumber of molelcules
Total (without water)20,7401
Polymers20,7401
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Protein elutes as a Monomer in the Gel Filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.296, 67.296, 108.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Isopeptide-forming domain-containing fimbrial protein


Mass: 20740.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A truncated form of Shaft pilin EbpC, refers to database WP_002388874.1
Source: (gene. exp.) Enterococcus faecalis OG1RF (bacteria) / Gene: EbpC / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.71 Å3/Da / Density % sol: 27.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM CHES-NaOH, pH 9.5 30% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→51.37 Å / Num. obs: 9867 / % possible obs: 94.4 % / Redundancy: 34.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.012 / Rrim(I) all: 0.073 / Net I/σ(I): 30.3
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 32.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 493 / CC1/2: 0.94 / Rpim(I) all: 0.1 / Rrim(I) all: 0.61 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→51.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.345 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24192 502 5.1 %RANDOM
Rwork0.1834 ---
obs0.18636 9365 94.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.633 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.44 Å20 Å2
2--0.87 Å2-0 Å2
3----2.83 Å2
Refinement stepCycle: 1 / Resolution: 1.99→51.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 0 38 1068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121050
X-RAY DIFFRACTIONr_bond_other_d0.0010.016992
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.8311423
X-RAY DIFFRACTIONr_angle_other_deg0.5151.7572284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1075138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.32851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70210170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
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_it10.2094.125558
X-RAY DIFFRACTIONr_mcbond_other10.1474.124558
X-RAY DIFFRACTIONr_mcangle_it15.0047.385694
X-RAY DIFFRACTIONr_mcangle_other15.0077.386695
X-RAY DIFFRACTIONr_scbond_it10.6284.436492
X-RAY DIFFRACTIONr_scbond_other10.624.44493
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.8617.922730
X-RAY DIFFRACTIONr_long_range_B_refined23.348.614164
X-RAY DIFFRACTIONr_long_range_B_other23.27748.64153
X-RAY DIFFRACTIONr_rigid_bond_restr3.59232042
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 40 -
Rwork0.182 715 -
obs--99.34 %

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