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- PDB-6m7c: Crystal structure of C-terminal fragment of pilus adhesin SpaC fr... -

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Basic information

Entry
Database: PDB / ID: 6m7c
TitleCrystal structure of C-terminal fragment of pilus adhesin SpaC from Lactobacillus rhamnosus GG
ComponentsPilus assembly protein
KeywordsCELL ADHESION / Pilus adhesin / Tip pilin / SpaCBA pilus / sortase / Lactobacillus rhamnosus GG / pili / fimbria / Probiotics / SpaC / surface protein
Function / homology
Function and homology information


Prealbumin-like fold domain / Prealbumin-like fold domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / 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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / 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: 3.18 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 18, 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 1.2Aug 26, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 9, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 15, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 1.5Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)29,3461
Polymers29,3461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.244, 58.559, 166.764
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: 29346.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Gene: CCE29_04955 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: A0A1Y0DVK9
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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 15%w/v PEG 6000, 5% w/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87782 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87782 Å / Relative weight: 1
ReflectionResolution: 3.18→55.25 Å / Num. obs: 6676 / % possible obs: 94.4 % / Redundancy: 8.3 % / Biso Wilson estimate: 94.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.042 / Net I/σ(I): 10.3
Reflection shellResolution: 3.18→3.26 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 335 / CC1/2: 0.787 / Rpim(I) all: 0.262 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M3Y

6m3y


Resolution: 3.18→55.25 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.873 / SU B: 57.655 / SU ML: 0.446 / Cross valid method: THROUGHOUT / ESU R Free: 0.547
RfactorNum. reflection% reflectionSelection details
Rfree0.31822 360 5.4 %RANDOM
Rwork0.26448 ---
obs0.26735 6315 91.61 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 95.991 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å2-0 Å2-0 Å2
2---7.72 Å20 Å2
3---5.39 Å2
Refinement stepCycle: 1 / Resolution: 3.18→55.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 0 0 1673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0111715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.041.6462359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2095261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80525.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.26915160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg36.05151
X-RAY DIFFRACTIONr_chiral_restr0.1320.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021348
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.9115.5531047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.5088.331307
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2775.055668
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.88399.9346699
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.18→3.26 Å
RfactorNum. reflection% reflection
Rfree0.367 22 -
Rwork0.354 315 -
obs--64.31 %
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)
17.3557-0.5223-1.96823.0855-0.53135.08380.12480.88570.3353-0.0680.0972-0.1669-0.1725-0.2494-0.22190.0983-0.07620.00290.71750.09590.0349-11.835-12.12-12.876
23.4633-2.9652-3.61765.28435.337310.4110.31870.22150.30180.202-0.0838-0.10090.3573-0.3061-0.23490.41020.05570.06271.0798-0.22040.094816.091-30.414-42.95
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A596 - 731
2X-RAY DIFFRACTION2A732 - 856

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