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

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Basic information

Entry
Database: PDB / ID: 5fgs
TitleCrystal structure of C-terminal domain of shaft pilin spaA from Lactobacillus rhamnosus GG - P21212 space group
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
Cell surface protein SpaA
Similarity search - Component
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 21, 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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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
B: Cell surface protein SpaA
C: Cell surface protein SpaA
D: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,81313
Polymers59,2244
Non-polymers5899
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-215 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.070, 74.343, 116.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA176 - 2982 - 124
21SERSERBB176 - 2982 - 124
12PROPROAA176 - 2972 - 123
22PROPROCC176 - 2972 - 123
13SERSERAA176 - 2982 - 124
23SERSERDD176 - 2982 - 124
14PROPROBB176 - 2972 - 123
24PROPROCC176 - 2972 - 123
15SERSERBB176 - 2982 - 124
25SERSERDD176 - 2982 - 124
16PROPROCC176 - 2972 - 123
26PROPRODD176 - 2972 - 123

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cell surface protein SpaA / pilus protein SpaA


Mass: 14806.058 Da / Num. of mol.: 4 / Fragment: C-terminal domain, residues 175-302
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.28 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES, 0.02M zinc sulphate, 25% PEG 550MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2→37.17 Å / Num. obs: 33984 / % possible obs: 99.3 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.9 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FGR

5fgr


Resolution: 2→37.17 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.611 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 1697 5 %RANDOM
Rwork0.21654 ---
obs0.21816 32254 99.15 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.744 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--1.6 Å20 Å2
3----2.02 Å2
Refinement stepCycle: 1 / Resolution: 2→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 9 256 3993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023792
X-RAY DIFFRACTIONr_bond_other_d0.0050.023395
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9415129
X-RAY DIFFRACTIONr_angle_other_deg1.01937863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75626.136176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86915608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.232158
X-RAY DIFFRACTIONr_chiral_restr0.0610.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024399
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02833
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_it0.8551.5231968
X-RAY DIFFRACTIONr_mcbond_other0.8551.5231967
X-RAY DIFFRACTIONr_mcangle_it1.3952.2792453
X-RAY DIFFRACTIONr_mcangle_other1.3952.2792454
X-RAY DIFFRACTIONr_scbond_it0.9221.5921824
X-RAY DIFFRACTIONr_scbond_other0.9221.5931824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4712.3572677
X-RAY DIFFRACTIONr_long_range_B_refined6.45313.014328
X-RAY DIFFRACTIONr_long_range_B_other6.39512.614268
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A67500.07
12B67500.07
21A66810.07
22C66810.07
31A67350.07
32D67350.07
41B66030.09
42C66030.09
51B68610.07
52D68610.07
61C66390.07
62D66390.07
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 116 -
Rwork0.296 2236 -
obs--94.95 %
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)
13.10140.9473-0.14913.69950.35932.5168-0.0329-0.16310.2029-0.2201-0.01520.4543-0.20820.03370.04820.0403-0.0071-0.03430.02610.0080.276816.6098.71248.984
21.8272-0.16450.92653.2212-1.46936.3572-0.00330.2265-0.1262-0.7272-0.211-0.2370.62380.30220.21420.21010.03890.07820.06110.04250.269313.194-17.71436.392
32.0076-0.3095-0.09854.04150.57285.47010.02370.15210.1347-0.0123-0.115-0.2025-0.41030.25930.09140.3817-0.0965-0.06930.1190.06250.254917.94121.19322.131
42.21221.0490.22559.2822-2.55093.7888-0.13330.21830.102-0.52940.0483-0.16960.1454-0.03290.08510.46950.02580.11540.2725-0.00580.213513.564-5.2339.674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A176 - 298
2X-RAY DIFFRACTION2B176 - 298
3X-RAY DIFFRACTION3C175 - 298
4X-RAY DIFFRACTION4D176 - 298

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