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- PDB-8kcl: Crystal Structure of M- and C-Domains of the shaft pilin LrpA fro... -

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Basic information

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


extracellular region / membrane
Similarity search - Function
: / 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
LPXTG-motif cell wall anchor domain protein
Similarity search - Component
Biological speciesLigilactobacillus ruminis ATCC 25644 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 8, 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


Theoretical massNumber of molelcules
Total (without water)28,1391
Polymers28,1391
Non-polymers00
Water5,224290
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)36.334, 47.677, 51.720
Angle α, β, γ (deg.)107.25, 101.52, 111.78
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 28139.395 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) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: E7FRT5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Sulphate, 0.1 M Tris pH 8.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9803 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9803 Å / Relative weight: 1
ReflectionResolution: 1.465→39.46 Å / Num. obs: 47229 / % possible obs: 95.2 % / Redundancy: 3.4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.069 / Rrim(I) all: 0.13 / Net I/σ(I): 6.9
Reflection shellResolution: 1.465→1.491 Å / Redundancy: 3 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2307 / CC1/2: 0.792 / Rpim(I) all: 0.308 / Rrim(I) all: 0.545 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→39.46 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.293 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19106 2321 4.9 %RANDOM
Rwork0.17464 ---
obs0.17545 44908 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0.26 Å2-0.28 Å2
2---0.29 Å2-0.15 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.47→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 0 290 2266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122023
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161906
X-RAY DIFFRACTIONr_angle_refined_deg1.61.6622743
X-RAY DIFFRACTIONr_angle_other_deg0.5551.5844419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.49451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.75610355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022336
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02418
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_it0.9930.8871042
X-RAY DIFFRACTIONr_mcbond_other0.9910.8871042
X-RAY DIFFRACTIONr_mcangle_it1.4991.591303
X-RAY DIFFRACTIONr_mcangle_other1.4981.5911304
X-RAY DIFFRACTIONr_scbond_it1.7021.07981
X-RAY DIFFRACTIONr_scbond_other1.7011.072982
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5981.871440
X-RAY DIFFRACTIONr_long_range_B_refined3.811.282200
X-RAY DIFFRACTIONr_long_range_B_other3.6249.282126
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.503 Å
RfactorNum. reflection% reflection
Rfree0.24 162 -
Rwork0.227 3285 -
obs--93.11 %
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)
10.19360.0851-0.03821.75170.35380.41690.023-0.02660.0230.0796-0.01440.0026-0.015-0.0292-0.00860.0084-0.00310.00060.01380.00260.0072-9.52925.613324.9799
20.7637-0.2486-0.08611.0102-0.020.7020.01510.0912-0.0615-0.0708-0.0280.03660.055-0.0370.01290.01-0.0021-0.00230.0154-0.00660.0056-11.4044-6.36738.5272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A208 - 343
2X-RAY DIFFRACTION2A344 - 466

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