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- PDB-5yxo: Crystal structure of shaft pilin spaD from Lactobacillus rhamnosu... -

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Basic information

Entry
Database: PDB / ID: 5yxo
TitleCrystal structure of shaft pilin spaD from Lactobacillus rhamnosus GG in bent conformation
ComponentsPilus assembly protein
KeywordsCELL ADHESION / Pilin / spaD / probiotic / isopeptide / SpaFED pili / adhesin
Function / homologyGram-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 / Immunoglobulin-like fold / Pilus assembly protein
Function and homology information
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsChaurasia, P. / Pratap, S. / Palva, A. / von Ossowski, I. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyBT/PR5891/BRB/10/1098/2012 India
CitationJournal: Commun Biol / Year: 2018
Title: Bent conformation of a backbone pilin N-terminal domain supports a three-stage pilus assembly mechanism.
Authors: Chaurasia, P. / Pratap, S. / Palva, A. / von Ossowski, I. / Krishnan, V.
History
DepositionDec 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)51,0411
Polymers51,0411
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.720, 73.720, 428.659
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Pilus assembly protein


Mass: 51040.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus GG (bacteria) / Strain: GG / Gene: CCE29_10230, PY66_09460 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): plysS / References: UniProt: A0A179XFF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.29 Å3/Da / Density meas: 2017498.625 Mg/m3 / Density % sol: 62.66 % / Description: three dimensional plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.51→71.55 Å / Num. obs: 19138 / % possible obs: 89.6 % / Redundancy: 9.1 % / Biso Wilson estimate: 61.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.048 / Rrim(I) all: 0.148 / Net I/σ(I): 10.6
Reflection shellResolution: 2.512→2.705 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 957 / CC1/2: 0.278 / Rpim(I) all: 0.466 / Rrim(I) all: 0.95 / % possible all: 45.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YU5, 5YXG

5yu5

5yxg


Resolution: 2.51→71.55 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 36.269 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R: 0.524 / ESU R Free: 0.342 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29095 986 5.2 %RANDOM
Rwork0.24074 ---
obs0.24325 18151 76.71 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 66 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.51→71.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 0 24 3213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193253
X-RAY DIFFRACTIONr_bond_other_d0.0010.022967
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9434419
X-RAY DIFFRACTIONr_angle_other_deg0.83636894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55325.385143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83215528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8211510
X-RAY DIFFRACTIONr_chiral_restr0.0660.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02625
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_it0.9044.5511656
X-RAY DIFFRACTIONr_mcbond_other0.9054.5511655
X-RAY DIFFRACTIONr_mcangle_it1.5616.8272063
X-RAY DIFFRACTIONr_mcangle_other1.5616.8272064
X-RAY DIFFRACTIONr_scbond_it0.9214.6661597
X-RAY DIFFRACTIONr_scbond_other0.924.6661598
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6026.9532356
X-RAY DIFFRACTIONr_long_range_B_refined2.89453.1893386
X-RAY DIFFRACTIONr_long_range_B_other2.88653.1823385
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.512→2.577 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 7 -
Rwork0.331 108 -
obs--6.47 %
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)
14.5784-0.85080.18656.3120.45945.5953-0.1935-0.1319-0.13450.5203-0.2328-0.48740.20190.16150.42640.1457-0.0151-0.06740.02630.06960.236639.653-11.7892.483
22.7306-1.88770.17985.9841-1.3031.442-0.1804-0.2463-0.10760.15880.17570.07410.1326-0.11870.00470.06670.0248-0.00260.04570.00160.048522.144-29.115-8.242
33.8255-3.32861.09786.494-0.10494.98170.0786-0.19510.08870.09320.0189-0.159-0.2529-0.1165-0.09750.05160.01270.01180.0570.03630.0598.3793.907-22.534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 181
2X-RAY DIFFRACTION2A182 - 358
3X-RAY DIFFRACTION3A359 - 481

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