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- PDB-5f44: Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG -

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Basic information

Entry
Database: PDB / ID: 5f44
TitleCrystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG
ComponentsCell surface protein SpaA
KeywordsCELL ADHESION / Pilin / spaA / probiotic / isopeptide / SpaCBA pili / adhesin
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
ACETATE ION / Cell surface protein SpaA
Similarity search - Component
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 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 3, 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 1.2Oct 16, 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
B: Cell surface protein SpaA
C: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3486
Polymers92,1703
Non-polymers1773
Water15,205844
1
A: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7832
Polymers30,7231
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area13530 Å2
MethodPISA
2
B: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7832
Polymers30,7231
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area13600 Å2
MethodPISA
3
C: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7832
Polymers30,7231
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.970, 63.200, 104.270
Angle α, β, γ (deg.)90.00, 95.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-745-

HOH

21C-740-

HOH

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Components

#1: Protein Cell surface protein SpaA / shaft Pilin spaA


Mass: 30723.498 Da / Num. of mol.: 3 / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 4.32 Å3/Da / Density % sol: 71.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.35 M trisodium citrate, 14% PEG 3350

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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: Jul 20, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.904→31.16 Å / Num. obs: 105419 / % possible obs: 90 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.91
Reflection shellResolution: 1.904→1.972 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.14 / % possible all: 63

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
Cootmodel building
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PHS

3phs


Resolution: 1.904→31.156 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 4223 5.02 %Random selection
Rwork0.1743 ---
obs0.1764 84062 72.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.904→31.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5971 0 12 844 6827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086124
X-RAY DIFFRACTIONf_angle_d1.1258330
X-RAY DIFFRACTIONf_dihedral_angle_d12.0372140
X-RAY DIFFRACTIONf_chiral_restr0.046938
X-RAY DIFFRACTIONf_plane_restr0.0061087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9042-1.92590.340350.2009106X-RAY DIFFRACTION3
1.9259-1.94850.2035210.2202335X-RAY DIFFRACTION9
1.9485-1.97230.395380.2208714X-RAY DIFFRACTION19
1.9723-1.99720.2683510.2288962X-RAY DIFFRACTION27
1.9972-2.02350.2657440.23081230X-RAY DIFFRACTION33
2.0235-2.05120.2789760.2261433X-RAY DIFFRACTION39
2.0512-2.08050.2512910.20481605X-RAY DIFFRACTION44
2.0805-2.11160.2524840.21061794X-RAY DIFFRACTION49
2.1116-2.14460.24721090.2071906X-RAY DIFFRACTION53
2.1446-2.17970.23661310.20242113X-RAY DIFFRACTION57
2.1797-2.21730.26071130.20612320X-RAY DIFFRACTION63
2.2173-2.25760.24351580.20662390X-RAY DIFFRACTION66
2.2576-2.3010.24431380.21472610X-RAY DIFFRACTION72
2.301-2.3480.26751460.2192815X-RAY DIFFRACTION76
2.348-2.3990.24411680.22752978X-RAY DIFFRACTION82
2.399-2.45480.23481700.22363142X-RAY DIFFRACTION87
2.4548-2.51610.26971760.2263406X-RAY DIFFRACTION92
2.5161-2.58410.25532110.21943565X-RAY DIFFRACTION99
2.5841-2.66010.26421990.21713670X-RAY DIFFRACTION100
2.6601-2.7460.27441920.22183706X-RAY DIFFRACTION100
2.746-2.8440.27622130.21843603X-RAY DIFFRACTION100
2.844-2.95780.25321780.2073696X-RAY DIFFRACTION100
2.9578-3.09230.28771780.19613689X-RAY DIFFRACTION100
3.0923-3.25520.22421690.18393674X-RAY DIFFRACTION100
3.2552-3.45890.23291810.16233708X-RAY DIFFRACTION100
3.4589-3.72560.17841840.14283729X-RAY DIFFRACTION100
3.7256-4.09970.16272060.12523671X-RAY DIFFRACTION100
4.0997-4.69120.14321910.10823724X-RAY DIFFRACTION100
4.6912-5.90390.13812040.10973734X-RAY DIFFRACTION100
5.9039-31.16010.15561980.13333811X-RAY DIFFRACTION99
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)
13.15470.06231.13790.46650.05891.7344-0.0968-0.0451-0.0555-0.0170.02020.0862-0.072-0.14570.06090.02890.0530.00230.1425-0.01750.0906-22.395321.764851.0249
21.0953-0.40570.86210.7973-0.8362.8563-0.1153-0.01360.22950.0806-0.0335-0.0969-0.44460.21390.12630.249-0.0146-0.07170.04090.00390.1482-38.938338.464119.7504
31.4210.75440.83781.45610.79812.8759-0.0152-0.11070.1675-0.1226-0.02020.0626-0.3029-0.01320.03270.1479-0.0706-0.00140.0774-0.05930.1017-59.065713.96215.6891
41.02330.17830.75441.28750.97855.2967-0.0122-0.2077-0.06720.24420.02570.10190.2812-0.4815-0.0110.11870.00590.01920.2634-0.04470.1076-53.650716.165254.4878
52.3704-0.37921.54161.096-0.04814.09260.10060.0042-0.17370.01450.0611-0.03560.13650.2786-0.10620.24720.0714-0.05430.2295-0.07450.1122-28.668621.4303-13.6878
61.39920.06331.38770.7622-0.12033.88060.0517-0.025-0.0571-0.187-0.0811-0.02050.08670.02740.02120.11860.03790.02660.2234-0.04640.0719-4.636417.76717.4407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 175 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 176 through 302 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 39 through 175 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 176 through 302 )B0
5X-RAY DIFFRACTION5chain 'C' and (resid 39 through 175 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 176 through 302 )C0

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