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- PDB-8kb2: Crystal Structure of M- and C-Domains of the shaft pilin LrpA fro... -

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Basic information

Entry
Database: PDB / ID: 8kb2
TitleCrystal Structure of M- and C-Domains of the shaft pilin LrpA from Ligilactobacillus ruminis - iodide derivative
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
IODIDE ION / LPXTG-motif cell wall anchor domain protein
Similarity search - Component
Biological speciesLigilactobacillus ruminis ATCC 25644 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 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 3, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,71820
Polymers28,7401
Non-polymers1,97719
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.903, 50.898, 125.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 28740.119 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

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Non-polymers , 6 types, 166 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 25% 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: 1.5498 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: 1.5498 Å / Relative weight: 1
ReflectionResolution: 1.905→39.58 Å / Num. obs: 21167 / % possible obs: 97.6 % / Redundancy: 48.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.018 / Rrim(I) all: 0.13 / Net I/σ(I): 24.2
Reflection shellResolution: 1.905→1.945 Å / Redundancy: 45.5 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1058 / CC1/2: 0.969 / Rpim(I) all: 0.141 / % possible all: 85.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→39.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.982 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21149 1052 5 %RANDOM
Rwork0.17949 ---
obs0.1811 20115 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0 Å2-0 Å2
2--0.08 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.91→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 32 147 2202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122073
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161972
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.6642800
X-RAY DIFFRACTIONr_angle_other_deg0.4661.5854572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0225264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.74851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91710364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022359
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
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_it1.2591.1691059
X-RAY DIFFRACTIONr_mcbond_other1.2591.1691059
X-RAY DIFFRACTIONr_mcangle_it1.9612.091322
X-RAY DIFFRACTIONr_mcangle_other1.962.0891323
X-RAY DIFFRACTIONr_scbond_it2.6171.5791014
X-RAY DIFFRACTIONr_scbond_other2.6161.581015
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2722.6881479
X-RAY DIFFRACTIONr_long_range_B_refined5.81214.42190
X-RAY DIFFRACTIONr_long_range_B_other5.81114.412191
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.954 Å
RfactorNum. reflection% reflection
Rfree0.264 69 -
Rwork0.212 1217 -
obs--82.86 %
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)
10.4743-0.0643-0.49350.492-0.17954.2925-0.0006-0.06470.0218-0.0050.06320.04360.0039-0.0878-0.06260.0608-0.00860.0070.0401-0.00460.048514.5448-1.945185.9494
21.98420.4919-0.91161.1017-0.25551.9377-0.04120.053-0.0138-0.09060.0495-0.04450.00320.0227-0.00820.06220.0058-0.00850.0088-0.00370.005226.06854.242451.5317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A208 - 343
2X-RAY DIFFRACTION2A344 - 472

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