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- PDB-8wgg: Crystal structure of basal pilin PilB from Streptococcus sanguinis -

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Basic information

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


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 / ACETIC ACID / FORMIC ACID / FimA fimbrial subunit-like protein, putative
Similarity search - Component
Biological speciesStreptococcus sanguinis SK36 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 basal pilin PilB from Streptococcus sanguinis
Authors: Yadav, S. / Parijat, P. / Krishnan, V.
History
DepositionSep 21, 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)49,25413
Polymers48,6191
Non-polymers63512
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.911, 58.630, 212.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 48619.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis SK36 (bacteria)
Gene: SSA_1633 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3CPB6

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Non-polymers , 6 types, 242 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8.5, 8% (w/v) PEG 4000 and 0.8 M Lithium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8713128 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8713128 Å / Relative weight: 1
ReflectionResolution: 1.878→45.207 Å / Num. obs: 30356 / % possible obs: 94.5 % / Redundancy: 8.9 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.055 / Net I/av σ(I): 9.3 / Net I/σ(I): 9.3
Reflection shellResolution: 1.878→1.937 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1518 / CC1/2: 0.887 / Rpim(I) all: 0.317 / % possible all: 92.3

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Processing

Software
NameVersionClassification
autoPROCdata reduction
MOLREP7.0.0.78phasing
Coot0.8.9.2model building
REFMAC7.0.078refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→45.2 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.431 / SU ML: 0.112 / Cross valid method: FREE R-VALUE / ESU R: 0.198 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1490 4.9 %RANDOM
Rwork0.19762 ---
obs0.19917 28866 77.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0 Å2
2---0.47 Å20 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.88→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 41 230 3446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123273
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163055
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.6654431
X-RAY DIFFRACTIONr_angle_other_deg0.3521.5717040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.186513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75610550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02733
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_it0.7550.9661678
X-RAY DIFFRACTIONr_mcbond_other0.7570.9671679
X-RAY DIFFRACTIONr_mcangle_it1.231.7232094
X-RAY DIFFRACTIONr_mcangle_other1.231.7232095
X-RAY DIFFRACTIONr_scbond_it1.1541.1371595
X-RAY DIFFRACTIONr_scbond_other1.1541.1351594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8731.992334
X-RAY DIFFRACTIONr_long_range_B_refined4.43113.0313621
X-RAY DIFFRACTIONr_long_range_B_other4.27912.8613484
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.926 Å
RfactorNum. reflection% reflection
Rfree0.263 71 -
Rwork0.225 1147 -
obs--42.95 %
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)
11.03280.05810.10722.1648-0.88194.17010.07280.0322-0.0634-0.0850.06870.10120.1208-0.1462-0.14150.0220.0045-0.02160.04990.00580.023431.705224.268317.671
20.81680.10740.6260.64330.09063.3371-0.0016-0.05260.0337-0.0232-0.03390.08850.0458-0.11120.03540.0758-0.0247-0.04240.01440.00710.033622.005517.722651.9582
30.69580.15590.3171.2112-0.82954.9055-0.1049-0.06710.1112-0.06530.05380.086-0.2857-0.03850.05110.0430.0072-0.02940.0593-0.02950.037330.530222.454288.4669
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 166
2X-RAY DIFFRACTION2A167 - 326
3X-RAY DIFFRACTION3A327 - 445

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