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

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Basic information

Entry
Database: PDB / ID: 6jbv
TitleCrystal structure of SpaE basal pilin from Lactobacillus rhamnosus GG - Selenium derivative
ComponentsPilus assembly protein
KeywordsCELL ADHESION / basal pilins / SpaFED pilus / isopeptide bonds / pilus anchoring / surface proteins / probiotic
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 / SAD / Resolution: 1.712 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
DepositionJan 26, 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_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pilus assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3254
Polymers45,2561
Non-polymers693
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.779, 63.936, 131.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pilus assembly protein / Cell wall anchoring pilin protein


Mass: 45255.945 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: plasmid / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): pLysS / References: UniProt: A0A345U425, UniProt: A0A5H1ZR38*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
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: 1.95 Å3/Da / Density % sol: 36 % / Description: Three dimensional plates
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, 30% (w/v) PEG 3350, 1 M sodium iodide, 0.1 M L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97868 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97868 Å / Relative weight: 1
ReflectionResolution: 1.712→65.556 Å / Num. obs: 38761 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.032 / Rrim(I) all: 0.086 / Net I/σ(I): 19.2
Reflection shellResolution: 1.712→1.741 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1960 / CC1/2: 0.793 / Rpim(I) all: 0.348 / Rrim(I) all: 0.951 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.712→65.556 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.344 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22312 1947 5 %RANDOM
Rwork0.19427 ---
obs0.19571 36810 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 31.362 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2--2.39 Å20 Å2
3----3.63 Å2
Refinement stepCycle: 1 / Resolution: 1.712→65.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 3 215 2553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132389
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172175
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.6573237
X-RAY DIFFRACTIONr_angle_other_deg1.431.5775047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9735298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39722.302126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73415357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.221516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
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_it1.7771.7151204
X-RAY DIFFRACTIONr_mcbond_other1.7771.7131203
X-RAY DIFFRACTIONr_mcangle_it2.72.561498
X-RAY DIFFRACTIONr_mcangle_other2.6992.5611499
X-RAY DIFFRACTIONr_scbond_it2.3031.8791185
X-RAY DIFFRACTIONr_scbond_other2.3021.881186
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3922.7421739
X-RAY DIFFRACTIONr_long_range_B_refined5.26633.0419852
X-RAY DIFFRACTIONr_long_range_B_other5.18232.5159694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.712→1.756 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 154 -
Rwork0.256 2684 -
obs--100 %
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)
11.387-0.0651-0.74371.86420.25492.62-0.15620.0454-0.2625-0.08050.0408-0.09380.42540.09190.11550.08210.01060.03140.0082-0.01660.229914.43259.455119.894
21.17010.14180.15510.69120.46541.7528-0.0219-0.12240.1294-0.0002-0.0124-0.0135-0.1066-0.00770.03440.00820.0018-0.00640.0129-0.01060.199721.73457.49879.461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 217
2X-RAY DIFFRACTION2A218 - 374

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