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

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Basic information

Entry
Database: PDB / ID: 9lks
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: 1.79 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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6594
Polymers20,5511
Non-polymers1083
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein elutes as a Monomer in the Gel Filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.182, 68.182, 127.412
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: 20550.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal D1 domain 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM Sodium-citrate, 33% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.79→53.64 Å / Num. obs: 17123 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.021 / Rrim(I) all: 0.051 / Net I/σ(I): 19.3
Reflection shellResolution: 1.79→1.82 Å / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 856 / CC1/2: 0.76 / Rpim(I) all: 0.314 / Rrim(I) all: 0.752 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→53.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.947 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21851 831 4.9 %RANDOM
Rwork0.16535 ---
obs0.16778 16292 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0.29 Å2-0 Å2
2---0.58 Å2-0 Å2
3---1.89 Å2
Refinement stepCycle: 1 / Resolution: 1.79→53.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 6 84 1102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121032
X-RAY DIFFRACTIONr_bond_other_d0.0010.016978
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.8271399
X-RAY DIFFRACTIONr_angle_other_deg0.5271.7512252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.25851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46810165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02206
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_it8.0992.922545
X-RAY DIFFRACTIONr_mcbond_other8.0862.922545
X-RAY DIFFRACTIONr_mcangle_it12.0745.219676
X-RAY DIFFRACTIONr_mcangle_other12.0815.224677
X-RAY DIFFRACTIONr_scbond_it9.9843.202487
X-RAY DIFFRACTIONr_scbond_other9.9763.205488
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.4015.72724
X-RAY DIFFRACTIONr_long_range_B_refined18.48234.654173
X-RAY DIFFRACTIONr_long_range_B_other18.07934.534125
X-RAY DIFFRACTIONr_rigid_bond_restr3.91232010
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.791→1.838 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 65 -
Rwork0.201 1129 -
obs--97.23 %

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