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

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Basic information

Entry
Database: PDB / ID: 6jch
TitleCrystal structure of SpaE basal pilin from Lactobacillus rhamnosus GG - Orthorhombic form
ComponentsPilus assembly protein
KeywordsCELL ADHESION / basal pilins / SpaFED pilus / isopeptide bonds / pilus anchoring / surface proteins / probiotic / sortase
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 GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.536 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 28, 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 / struct_conn_type
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 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: 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)44,9034
Polymers44,8341
Non-polymers693
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.382, 63.523, 130.245
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 / SpaE


Mass: 44833.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus GG (bacteria) / Gene: DU507_12320 / Variant: ATCC 53103 / GG / Plasmid: pET28b(+) / 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.: 385 / 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: 1.9 Å3/Da / Density % sol: 35.37 % / Description: Three dimensional plate shaped crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M bis-tris propane pH 8.5, 0.25 M sodium formate, 25% (w/v) PEG 3350, 0.2 M sodium iodide, 0.02 M L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.536→57.094 Å / Num. obs: 52018 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 21.3
Reflection shellResolution: 1.536→1.562 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2453 / CC1/2: 0.832 / Rpim(I) all: 0.261 / Rrim(I) all: 0.568 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JBV

6jbv


Resolution: 1.536→23.736 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.37
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2504 4.82 %RANDOM
Rwork0.1797 ---
obs0.1816 51994 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.536→23.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 3 385 2897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062563
X-RAY DIFFRACTIONf_angle_d0.8473479
X-RAY DIFFRACTIONf_dihedral_angle_d5.5291552
X-RAY DIFFRACTIONf_chiral_restr0.055379
X-RAY DIFFRACTIONf_plane_restr0.006465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5358-1.56530.24971460.23652576X-RAY DIFFRACTION97
1.5653-1.59730.2451190.22652746X-RAY DIFFRACTION99
1.5973-1.6320.24871260.20492722X-RAY DIFFRACTION100
1.632-1.670.23281490.18632714X-RAY DIFFRACTION100
1.67-1.71170.22561470.18562716X-RAY DIFFRACTION100
1.7117-1.7580.20941480.18562700X-RAY DIFFRACTION100
1.758-1.80970.21421350.182751X-RAY DIFFRACTION100
1.8097-1.86810.24851600.19292694X-RAY DIFFRACTION100
1.8681-1.93480.22821310.19672724X-RAY DIFFRACTION100
1.9348-2.01220.25481190.17972751X-RAY DIFFRACTION100
2.0122-2.10380.19891450.1792735X-RAY DIFFRACTION100
2.1038-2.21460.21821450.17322748X-RAY DIFFRACTION100
2.2146-2.35320.22851330.18142763X-RAY DIFFRACTION100
2.3532-2.53480.22961430.18792770X-RAY DIFFRACTION100
2.5348-2.78950.21441430.18332782X-RAY DIFFRACTION100
2.7895-3.19230.22781270.18152807X-RAY DIFFRACTION100
3.1923-4.01880.18081500.16622817X-RAY DIFFRACTION100
4.0188-23.73870.22941380.17082974X-RAY DIFFRACTION100
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)
11.37720.02010.51081.67340.08692.0635-0.1532-0.12540.37150.20240.014-0.1265-0.46260.09580.08580.2155-0.0174-0.05740.1195-0.02970.234835.15824.89412.694
21.1727-0.1256-0.3710.86180.43251.8274-0.02830.0819-0.1487-0.0223-0.0177-0.01480.15270.00750.02580.1398-0.00390.00340.1408-0.0080.209542.17086.339651.8667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 375 )

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