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- PDB-5faa: Crystal structure of C-terminal domain of shaft pilin spaA from L... -

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Basic information

Entry
Database: PDB / ID: 5faa
TitleCrystal structure of C-terminal domain of shaft pilin spaA from Lactobacillus rhamnosus GG, - I422 space group
ComponentsCell surface protein SpaA
KeywordsCELL ADHESION / Pilin / spaA / probiotic / isopeptide / SpaCBA pili / adhesin / adhesion
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 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell surface protein SpaA
Similarity search - Component
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyBT/PR5891/BRB/10/1098/2012 India
CitationJournal: Sci Rep / Year: 2016
Title: New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit
Authors: Chaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / Krishnan, V.
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 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: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7862
Polymers30,7231
Non-polymers621
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.240, 100.240, 57.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

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Components

#1: Protein Cell surface protein SpaA


Mass: 30723.498 Da / Num. of mol.: 1 / Fragment: UNP residues 35-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus GG (bacteria) / Strain: GG / Gene: LRHM_0426 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: C7T9P4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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

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Sample preparation

CrystalDensity Matthews: 1.18 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M sodium acetate, 25% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→28.89 Å / Num. obs: 19599 / % possible obs: 99.9 % / Redundancy: 28.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 37
Reflection shellResolution: 1.6→1.75 Å / Redundancy: 29.1 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 6.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata processing
Aimlessdata scaling
MR-Rosettaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PHS

3phs


Resolution: 1.6→28.89 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.186 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15769 1001 5.1 %RANDOM
Rwork0.12972 ---
obs0.1311 18598 99.77 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.5 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.556 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.6→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 4 144 1079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02985
X-RAY DIFFRACTIONr_bond_other_d0.0010.02880
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9411336
X-RAY DIFFRACTIONr_angle_other_deg0.6932043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.18326.30446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.44615159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.676152
X-RAY DIFFRACTIONr_chiral_restr0.070.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
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_it1.1741.657511
X-RAY DIFFRACTIONr_mcbond_other1.1651.654510
X-RAY DIFFRACTIONr_mcangle_it1.5172.494644
X-RAY DIFFRACTIONr_mcangle_other1.5182.496645
X-RAY DIFFRACTIONr_scbond_it1.5861.968473
X-RAY DIFFRACTIONr_scbond_other1.5851.968473
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.032.851693
X-RAY DIFFRACTIONr_long_range_B_refined3.54215.7031185
X-RAY DIFFRACTIONr_long_range_B_other3.5415.7151186
X-RAY DIFFRACTIONr_rigid_bond_restr1.89831864
X-RAY DIFFRACTIONr_sphericity_free26.786552
X-RAY DIFFRACTIONr_sphericity_bonded9.2451938
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 70 -
Rwork0.148 1365 -
obs--99.72 %

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