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- PDB-6m3y: Crystal structure of pilus adhesin, SpaC from Lactobacillus rhamn... -

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Basic information

Entry
Database: PDB / ID: 6m3y
TitleCrystal structure of pilus adhesin, SpaC from Lactobacillus rhamnosus GG - open conformation
ComponentsPilus assembly protein
KeywordsCELL ADHESION / Pilus adhesin / Tip pilin / vWFA domain / SpaCBA pilus / sortase / Lactobacillus rhamnosus GG / Pili / Fimbria / Probiotics / SpaC / lectin / surface protein.
Function / homology
Function and homology information


Prealbumin-like fold domain / Prealbumin-like fold domain / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...Prealbumin-like fold domain / Prealbumin-like fold domain / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pilus assembly protein
Similarity search - Component
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKant, A. / Palva, A. / von Ossowski, I. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5891/BRB/10/1098/2012 India
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Crystal structure of lactobacillar SpaC reveals an atypical five-domain pilus tip adhesin: Exposing its substrate-binding and assembly in SpaCBA pili.
Authors: Kant, A. / Palva, A. / von Ossowski, I. / Krishnan, V.
History
DepositionMar 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Sep 15, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pilus assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2442
Polymers89,2201
Non-polymers241
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-7 kcal/mol
Surface area37510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.045, 110.023, 128.344
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 Pilus assembly protein


Mass: 89219.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Gene: CCE29_04955 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A1Y0DVK9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M sodium sulphate, 0.1 M Bis-Tris propane pH 6.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.93→83.531 Å / Num. obs: 52205 / % possible obs: 83.8 % / Redundancy: 4 % / Biso Wilson estimate: 28.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.029 / Net I/σ(I): 14.3
Reflection shellResolution: 1.93→2.042 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2611 / CC1/2: 0.732 / Rpim(I) all: 0.352

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→83.53 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.771 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24757 2597 5 %RANDOM
Rwork0.2066 ---
obs0.2086 49612 59.75 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.77 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.93→83.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6179 0 1 99 6279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196327
X-RAY DIFFRACTIONr_bond_other_d0.0010.025518
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.8668598
X-RAY DIFFRACTIONr_angle_other_deg1.0262.9312917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83726.376298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.547151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8231516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021172
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_it1.6272.133241
X-RAY DIFFRACTIONr_mcbond_other1.6272.133240
X-RAY DIFFRACTIONr_mcangle_it2.5463.1894046
X-RAY DIFFRACTIONr_mcangle_other2.5463.1894047
X-RAY DIFFRACTIONr_scbond_it2.1342.2813086
X-RAY DIFFRACTIONr_scbond_other2.1342.2813084
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2843.3484552
X-RAY DIFFRACTIONr_long_range_B_refined4.74124.5176602
X-RAY DIFFRACTIONr_long_range_B_other4.74124.5116600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.976 Å
RfactorNum. reflection% reflection
Rfree0.305 39 -
Rwork0.336 920 -
obs--14.98 %
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)
12.082-0.222-0.98331.28610.43532.460.0742-0.12170.13350.1716-0.0458-0.21170.08270.1355-0.02840.1486-0.0409-0.0230.02320.00050.163935.7390.005-10.074
22.10990.44540.22521.91910.99893.2734-0.00990.07260.0154-0.0357-0.04280.03920.135-0.09290.05260.0189-0.0048-0.01850.00660.00350.056422.86714.38536.882
33.12640.1863.09810.66220.09086.7424-0.0084-0.05060.27350.02-0.05010.0228-0.1491-0.08210.05840.1510.0363-0.06240.0867-0.030.243544.20920.72774.974
43.4570.20060.07263.5704-0.95143.51130.2424-0.0489-0.4610.1342-0.0643-0.20570.4730.2016-0.17810.12680.0436-0.08780.027-0.01090.19168.71811.74697.742
51.5901-0.3119-0.71421.02411.00464.9628-0.01170.37420.2038-0.2914-0.010.1981-0.3426-0.28170.02170.30160.0098-0.06970.24550.07120.297679.6037.825139.347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A129 - 385
2X-RAY DIFFRACTION2A36 - 128
3X-RAY DIFFRACTION2A386 - 493
4X-RAY DIFFRACTION3A494 - 597
5X-RAY DIFFRACTION4A598 - 731
6X-RAY DIFFRACTION5A732 - 857

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