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- PDB-8wxd: Crystal Structure of shaft pilin PilA from Streptococcus sanguinis -

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Basic information

Entry
Database: PDB / ID: 8wxd
TitleCrystal Structure of shaft pilin PilA from Streptococcus sanguinis
ComponentsSurface protein, putative
KeywordsSTRUCTURAL PROTEIN / Shaft pilin / Backbone pilin / Isopeptide / Oral biofilm / Dental plaque / primary colonizer / sortase pili / Bacterial adhesion / Fimbrial subunit
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
: / Surface protein, putative
Similarity search - Component
Biological speciesStreptococcus sanguinis SK36 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 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 shaft pilin PilA from Streptococcus sanguinis
Authors: Yadav, S. / Parijat, P. / Krishnan, V.
History
DepositionOct 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Surface protein, putative
B: Surface protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,80718
Polymers97,6752
Non-polymers1,13216
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.593, 89.949, 216.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Surface protein, putative


Mass: 48837.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis SK36 (bacteria)
Gene: SSA_1632 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3CPB5

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Non-polymers , 6 types, 50 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 0.01 M Cadmium Sulphate, 1.0 M Sodium acetate tri-hydrate.
PH range: 7.5 / Temp details: RT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.995→58.35 Å / Num. obs: 36257 / % possible obs: 87.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.2 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.054 / Net I/σ(I): 7.8
Reflection shellResolution: 1.995→2.159 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5501 / CC1/2: 0.592 / Rpim(I) all: 0.379 / % possible all: 90.5

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Processing

Software
NameVersionClassification
XDS5.8.0258data reduction
PHASER7.0.0.78phasing
Coot0.8.9.2model building
REFMAC7.0.0.78refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.995→58.35 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.976 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25936 1854 5.1 %RANDOM
Rwork0.2093 ---
obs0.21184 34403 87.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.359 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å20 Å2
2--0.33 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.995→58.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6412 0 29 34 6475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136581
X-RAY DIFFRACTIONr_bond_other_d0.0370.0175852
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.6558939
X-RAY DIFFRACTIONr_angle_other_deg2.8111.57413658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0885844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.40724.934304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.564151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8561516
X-RAY DIFFRACTIONr_chiral_restr0.070.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027434
X-RAY DIFFRACTIONr_gen_planes_other0.0440.021286
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_it1.7832.9893364
X-RAY DIFFRACTIONr_mcbond_other1.7832.9883363
X-RAY DIFFRACTIONr_mcangle_it3.0964.4794206
X-RAY DIFFRACTIONr_mcangle_other3.0964.4794207
X-RAY DIFFRACTIONr_scbond_it1.9143.153217
X-RAY DIFFRACTIONr_scbond_other1.9143.1513218
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2114.6474732
X-RAY DIFFRACTIONr_long_range_B_refined6.41555.3926782
X-RAY DIFFRACTIONr_long_range_B_other6.41555.39526779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.995→2.047 Å
RfactorNum. reflection% reflection
Rfree0.359 29 -
Rwork0.263 502 -
obs--8.88 %
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)
10.07170.1514-0.26680.5412-0.08092.1275-0.0333-0.0249-0.0368-0.0156-0.0802-0.09160.23350.01510.11340.05840.0030.02160.03770.01460.023135.2053116.68263.4499
20.0433-0.0255-0.22950.28890.46641.81360.00370.024-0.0186-0.0002-0.08360.024-0.0919-0.2030.07990.03050.00760.0110.0634-0.01620.014730.5599126.8357-31.4829
30.2222-0.0068-0.14690.03510.2732.3478-0.0370.00610.05280.0183-0.02730.0120.1882-0.16160.06430.0432-0.02320.00390.0449-0.0150.019934.245112.6544-67.8899
40.4985-0.3912-0.14720.3196-0.02391.6552-0.08520.1349-0.13760.0667-0.10620.09630.0817-0.02290.19130.0472-0.01840.03840.0373-0.03430.054955.6268113.7639-118.4629
50.1802-0.0335-0.3070.1599-0.26211.47070.0021-0.02570.0012-0.0107-0.0245-0.0435-0.04780.08590.02240.0213-0.00180.02020.02930.0090.028158.3541126.7631-84.4182
60.22230.1359-0.21920.1061-0.32921.91180.0058-0.04050.0316-0.0161-0.04020.01080.19070.18070.03440.04830.04120.00690.06680.00650.010556.3004114.7281-47.1188
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 165
2X-RAY DIFFRACTION2A166 - 325
3X-RAY DIFFRACTION3A326 - 447
4X-RAY DIFFRACTION4B29 - 165
5X-RAY DIFFRACTION5B166 - 325
6X-RAY DIFFRACTION6B326 - 447

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