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- PDB-8w5b: Crystal Structure of the shaft pilin LrpA from Ligilactobacillus ... -

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Basic information

Entry
Database: PDB / ID: 8w5b
TitleCrystal Structure of the shaft pilin LrpA from Ligilactobacillus ruminis
ComponentsLPXTG-motif cell wall anchor domain protein
KeywordsCELL ADHESION / Backbone pilin / isopeptide bond / pili / gut bacteria / probiotic
Function / homology
Function and homology information


: / Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold
Similarity search - Domain/homology
IODIDE ION / LPXTG-motif cell wall anchor domain protein
Similarity search - Component
Biological speciesLigilactobacillus ruminis ATCC 25644 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsPrajapati, A. / Palva, A. / von Ossowski, I. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR22343/BRB/10/1570/2016 India
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis.
Authors: Prajapati, A. / Palva, A. / von Ossowski, I. / Krishnan, V.
History
DepositionAug 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPXTG-motif cell wall anchor domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3362
Polymers49,2091
Non-polymers1271
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.391, 47.391, 227.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein LPXTG-motif cell wall anchor domain protein


Mass: 49209.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Shaft pilin
Source: (gene. exp.) Ligilactobacillus ruminis ATCC 25644 (bacteria)
Gene: HMPREF0542_11612 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: E7FRT5
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.6, 15% PEG 3000, 5% polyvinylpyrrolidone K15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.268→75.804 Å / Num. obs: 26024 / % possible obs: 98.4 % / Redundancy: 10.3 % / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.012 / Rrim(I) all: 0.038 / Net I/σ(I): 27.9
Reflection shellResolution: 2.268→2.307 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1280 / CC1/2: 0.888 / Rpim(I) all: 0.264 / Rrim(I) all: 0.86 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→75.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.951 / SU B: 19.785 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24019 1305 5 %RANDOM
Rwork0.22227 ---
obs0.22332 24719 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20.97 Å2-0 Å2
2--1.93 Å2-0 Å2
3----6.27 Å2
Refinement stepCycle: 1 / Resolution: 2.27→75.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 1 13 3050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123090
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162899
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.6664195
X-RAY DIFFRACTIONr_angle_other_deg0.4271.586706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4375402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.35452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35410513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02639
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_it4.4255.1031614
X-RAY DIFFRACTIONr_mcbond_other4.4185.1031614
X-RAY DIFFRACTIONr_mcangle_it5.8959.142014
X-RAY DIFFRACTIONr_mcangle_other5.8939.1412015
X-RAY DIFFRACTIONr_scbond_it4.8765.4991476
X-RAY DIFFRACTIONr_scbond_other4.8745.51477
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.229.9382182
X-RAY DIFFRACTIONr_long_range_B_refined9.00249.213112
X-RAY DIFFRACTIONr_long_range_B_other9.00249.213113
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.27→2.327 Å
RfactorNum. reflection% reflection
Rfree0.366 84 -
Rwork0.316 1839 -
obs--99.53 %
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)
13.03570.0096-1.68341.29050.14753.8075-0.0315-0.1418-0.2097-0.23910.0706-0.11970.2940.136-0.03910.2454-0.16340.04230.38610.08480.472912.298426.971927.9069
21.67492.09691.62933.55722.05982.7926-0.047-0.1383-0.168-0.129-0.0412-0.1653-0.05390.12630.08820.5615-0.26510.26430.21570.00640.438210.243718.2289-5.5877
31.88841.17061.87552.37512.28143.920.1901-0.0980.073-0.1732-0.34860.2407-0.1892-0.39840.15860.5962-0.14070.18380.147-0.07440.3688-15.4399-2.5461-22.8055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 207
2X-RAY DIFFRACTION2A208 - 343
3X-RAY DIFFRACTION3A344 - 472

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