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- PDB-8wg6: Crystal structure of major pilin PilB from Streptococcus sanguini... -

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Basic information

Entry
Database: PDB / ID: 8wg6
TitleCrystal structure of major pilin PilB from Streptococcus sanguinis - SeMet derivative
ComponentsFimA fimbrial subunit-like protein, putative
KeywordsCELL ADHESION / Major Pilin / Bacterial adhesion / coaggregation / isopeptide bond / oral biofilm / dental plaque / sortase pili
Function / homology
Function and homology information


extracellular region / membrane
Similarity search - Function
Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Fimbrial isopeptide formation D2 domain / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / FimA fimbrial subunit-like protein, putative
Similarity search - Component
Biological speciesStreptococcus sanguinis SK36 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsYadav, S. / Parijat, P. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2019/000432 India
CitationJournal: To be published
Title: Crystal structure of major pilin PilB from Streptococcus sanguinis - SeMet derivative
Authors: Yadav, S. / Parijat, P. / Krishnan, V.
History
DepositionSep 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FimA fimbrial subunit-like protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1515
Polymers48,9481
Non-polymers2034
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.780, 58.772, 214.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FimA fimbrial subunit-like protein, putative


Mass: 48947.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis SK36 (bacteria)
Strain: SK36 / Gene: SSA_1633 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): E.coli / References: UniProt: A3CPB6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Potassium acetate, 0.1 M Hepes pH 7.0, 5% w/v polyvinyl alcohol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9803 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9803 Å / Relative weight: 1
ReflectionResolution: 2.399→56.677 Å / Num. obs: 19213 / % possible obs: 98.2 % / Redundancy: 46.5 % / CC1/2: 0.997 / Rpim(I) all: 0.054 / Net I/σ(I): 15.7
Reflection shellResolution: 2.399→2.447 Å / Redundancy: 46.8 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 961 / CC1/2: 0.918 / Rpim(I) all: 0.265 / % possible all: 86.3

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Processing

Software
NameVersionClassification
XDS5.8.0258data reduction
CRANK27.0.078phasing
Coot0.8.9.2model building
REFMAC7.0.0.78refinement
autoPROCdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→45.41 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.858 / SU B: 17.081 / SU ML: 0.195 / Cross valid method: FREE R-VALUE / ESU R: 0.457 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26939 934 4.9 %RANDOM
Rwork0.22615 ---
obs0.22828 18274 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.328 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0 Å2-0 Å2
2---0.18 Å20 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2.4→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 13 146 3335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123237
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163007
X-RAY DIFFRACTIONr_angle_refined_deg0.9731.6644394
X-RAY DIFFRACTIONr_angle_other_deg0.3151.5696925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9095418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.29513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99610524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0380.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02723
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_it0.5960.7491678
X-RAY DIFFRACTIONr_mcbond_other0.5540.7441675
X-RAY DIFFRACTIONr_mcangle_it0.9861.3352092
X-RAY DIFFRACTIONr_mcangle_other0.9861.3352093
X-RAY DIFFRACTIONr_scbond_it0.7720.8321559
X-RAY DIFFRACTIONr_scbond_other0.7710.8331560
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3651.4872303
X-RAY DIFFRACTIONr_long_range_B_refined3.2969.4613221
X-RAY DIFFRACTIONr_long_range_B_other3.239.4313175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.447 Å
RfactorNum. reflection% reflection
Rfree0.306 51 -
Rwork0.266 1161 -
obs--86.63 %
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)
11.26850.07880.27391.6103-1.18654.79590.06720.00880.0079-0.070.05470.04820.1317-0.2598-0.12190.08950.0103-0.01840.0702-0.00360.0275-4.677824.647317.9435
20.966-0.24860.39960.7106-0.28643.0865-0.0695-0.0751-0.0150.0795-0.06850.0109-0.0734-0.10380.1380.0841-0.0197-0.02470.02530.00130.0164-15.082518.302352.1999
30.91160.34820.24731.1968-0.39386.6206-0.15120.0120.139-0.09040.02770.0907-0.41460.05550.12350.10180.0183-0.04330.09270.00160.0517-7.018122.788489.5702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 166
2X-RAY DIFFRACTION2A167 - 326
3X-RAY DIFFRACTION3A327 - 447

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