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- PDB-6jk7: Crystal structure of SpaE basal pilin from Lactobacillus rhamnosu... -

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Basic information

Entry
Database: PDB / ID: 6jk7
TitleCrystal structure of SpaE basal pilin from Lactobacillus rhamnosus GG - Trigonal form
ComponentsPilus assembly protein
KeywordsCELL ADHESION / basal pilins / SpaFED pilus / isopeptide bonds / pilus anchoring / surface proteins / probiotic / sortase
Function / homology
Function and homology information


Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Prealbumin-like fold domain / Prealbumin-like fold domain / 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: 3.204 Å
AuthorsMegta, A.K. / Mishra, A.K. / Palva, A. / von Ossowski, I. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/PR5891/BRB/10/1098/2012 India
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Crystal structure of basal pilin SpaE reveals the molecular basis of its incorporation in the lactobacillar SpaFED pilus.
Authors: Megta, A.K. / Mishra, A.K. / Palva, A. / von Ossowski, I. / Krishnan, V.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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)44,8341
Polymers44,8341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.045, 130.045, 59.335
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Pilus assembly protein / SpaE


Mass: 44833.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (strain ATCC 53103 / GG) (bacteria)
Strain: ATCC 53103 / GG / Gene: DU507_12320 / Plasmid: pET28b(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): pLysS / References: UniProt: A0A345U425, UniProt: A0A5H1ZR38*PLUS
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: 3.22 Å3/Da / Density % sol: 61 % / Description: Three dimensional trigonal crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M bis-tris propane pH 8.5, 0.3 M sodium formate, 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97887 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 3.204→65.023 Å / Num. obs: 9728 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.029 / Rrim(I) all: 0.071 / Net I/σ(I): 19.3
Reflection shellResolution: 3.204→3.26 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 495 / CC1/2: 0.76 / Rpim(I) all: 0.321 / Rrim(I) all: 0.785 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JBV

6jbv


Resolution: 3.204→52.495 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.41
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 453 4.66 %RANDOM
Rwork0.2123 ---
obs0.2135 9717 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.204→52.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 0 0 2336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042403
X-RAY DIFFRACTIONf_angle_d1.0083275
X-RAY DIFFRACTIONf_dihedral_angle_d3.0321432
X-RAY DIFFRACTIONf_chiral_restr0.055364
X-RAY DIFFRACTIONf_plane_restr0.005435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2043-3.66790.28611550.24663053X-RAY DIFFRACTION100
3.6679-4.62080.23141420.21083061X-RAY DIFFRACTION100
4.6208-52.50210.22631560.20333150X-RAY DIFFRACTION100
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)
14.3818-0.93282.36193.860.9785.2193-0.00880.1667-0.394-0.38520.1692-0.18760.30770.1163-0.13090.4425-0.13330.06750.79650.04380.631645.5278-54.85213.6459
25.2417-0.00860.95512.06810.28343.5417-0.33351.21490.6289-0.1560.32940.0668-0.2704-0.3564-0.01330.6059-0.20020.04411.2120.23220.84897.1146-47.45190.8182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 372 )

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