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- PDB-7bvx: Crystal structure of C-terminal fragment of pilus adhesin SpaC fr... -

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Basic information

Entry
Database: PDB / ID: 7bvx
TitleCrystal structure of C-terminal fragment of pilus adhesin SpaC from Lactobacillus rhamnosus GG-Iodide soaked
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
Similarity search - Domain/homology
IODIDE ION / Pilus assembly protein
Similarity search - Component
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 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
DepositionApr 12, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 / 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)32,2797
Polymers31,5171
Non-polymers7616
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-1 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.045, 114.919, 122.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Pilus assembly protein


Mass: 31517.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MGSSHHHHHHSSGLVPRGSHMTNQQYGFQFQKKTTDGTDLSADQLKAMQFNLTQYSDNSF QQASKTNAITSTDLQALAPGYYGIQEAAAPTGYQLDGTTYLFQLTSDGQWQYHGTKDNVT SGSVINGQQTLNPVGDKSDDFTVTGDHQQILTLTKYDEPKPSMTLRVIKQDNQSQYLAGA ...Details: MGSSHHHHHHSSGLVPRGSHMTNQQYGFQFQKKTTDGTDLSADQLKAMQFNLTQYSDNSF QQASKTNAITSTDLQALAPGYYGIQEAAAPTGYQLDGTTYLFQLTSDGQWQYHGTKDNVT SGSVINGQQTLNPVGDKSDDFTVTGDHQQILTLTKYDEPKPSMTLRVIKQDNQSQYLAGA AFTLQPSAGEAETITSSATSEGQAFATKLVADGTYTMSETKAPDGYQSNPAKIAIQVATT GKEATVTIDGEALKPGESKNGYTLAIDGSTITLQAINQPLAILPLEHHHHHH
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
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
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: 3.51 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 2M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.4231 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4231 Å / Relative weight: 1
ReflectionResolution: 3.35→57.53 Å / Num. obs: 6345 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.016 / Net I/σ(I): 34.7
Reflection shellResolution: 3.35→3.41 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 324 / CC1/2: 0.88 / Rpim(I) all: 0.24 / % possible all: 100

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Processing

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

6m3y


Resolution: 3.36→57.46 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.856 / SU B: 44.209 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.624 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34573 295 4.6 %RANDOM
Rwork0.30479 ---
obs0.30677 6050 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 145.844 Å2
Baniso -1Baniso -2Baniso -3
1--9.31 Å2-0 Å20 Å2
2--3.38 Å2-0 Å2
3---5.93 Å2
Refinement stepCycle: 1 / Resolution: 3.36→57.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 7 0 1681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121716
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181338
X-RAY DIFFRACTIONr_angle_refined_deg1.931.6552357
X-RAY DIFFRACTIONr_angle_other_deg1.6241.5673079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2725259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.01125.76952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.74515174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.852151
X-RAY DIFFRACTIONr_chiral_restr0.0750.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022088
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02327
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_it7.71610.6541039
X-RAY DIFFRACTIONr_mcbond_other7.71410.6541038
X-RAY DIFFRACTIONr_mcangle_it11.83915.9771297
X-RAY DIFFRACTIONr_mcangle_other11.83615.9761298
X-RAY DIFFRACTIONr_scbond_it7.51910.442677
X-RAY DIFFRACTIONr_scbond_other7.51310.441678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.27115.6311061
X-RAY DIFFRACTIONr_long_range_B_refined17.4466697
X-RAY DIFFRACTIONr_long_range_B_other17.4476696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.36→3.444 Å
RfactorNum. reflection% reflection
Rfree0.37 29 -
Rwork0.29 438 -
obs--100 %
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)
16.25980.4956-2.1043.36431.14246.49740.15540.3658-0.0126-0.943-0.43480.35340.0831-0.85360.27950.41530.1093-0.13950.1476-0.0760.0706-12.2195-1.1877-16.3809
24.355-2.2683-1.99953.5720.7392.5066-0.071-0.2860.24230.34880.0244-0.565-0.7676-0.1590.04670.85590.1156-0.02030.394-0.19260.21877.5311-28.1925-46.5978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A597 - 732
2X-RAY DIFFRACTION2A733 - 856

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