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- PDB-5j4m: Crystal structure of shaft pilin SpaA from Lactobacillus rhamnosu... -

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Basic information

Entry
Database: PDB / ID: 5j4m
TitleCrystal structure of shaft pilin SpaA from Lactobacillus rhamnosus GG - E269A/D295N double mutant
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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
DepositionApr 1, 2016Deposition 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 / 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_oper_list.symmetry_operation / _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 13, 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


Theoretical massNumber of molelcules
Total (without water)91,9933
Polymers91,9933
Non-polymers00
Water12,286682
1
A: Cell surface protein SpaA


Theoretical massNumber of molelcules
Total (without water)30,6641
Polymers30,6641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell surface protein SpaA


Theoretical massNumber of molelcules
Total (without water)30,6641
Polymers30,6641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cell surface protein SpaA


Theoretical massNumber of molelcules
Total (without water)30,6641
Polymers30,6641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)229.700, 64.394, 105.049
Angle α, β, γ (deg.)90.00, 95.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 39 - 302 / Label seq-ID: 12 - 275

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Cell surface protein SpaA


Mass: 30664.479 Da / Num. of mol.: 3 / Fragment: UNP residues 35-302 / Mutation: E269A, D295N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 4.2 Å3/Da / Density % sol: 70.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Sodium/Potassium tartrate, 100mM Tris buffer, 200mM Lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97876 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 1.99→104.58 Å / Num. obs: 103663 / % possible obs: 99.3 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.6
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata processing
MOLREPphasing
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F44

5f44


Resolution: 1.99→104.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.893 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22817 5306 5.1 %RANDOM
Rwork0.20511 ---
obs0.20631 98294 99.1 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 46.901 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.48 Å2
2--0.81 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.99→104.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5963 0 0 682 6645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.026097
X-RAY DIFFRACTIONr_bond_other_d0.0080.025531
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9368290
X-RAY DIFFRACTIONr_angle_other_deg1.335312769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.9225.522268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12215932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4921515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027049
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021372
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_it1.5791.513136
X-RAY DIFFRACTIONr_mcbond_other1.5791.513135
X-RAY DIFFRACTIONr_mcangle_it2.392.2553913
X-RAY DIFFRACTIONr_mcangle_other2.392.2553914
X-RAY DIFFRACTIONr_scbond_it2.6561.7752961
X-RAY DIFFRACTIONr_scbond_other2.6561.7752962
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0322.5394378
X-RAY DIFFRACTIONr_long_range_B_refined9.86514.7167124
X-RAY DIFFRACTIONr_long_range_B_other9.87613.2926824
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)
11A285020.09
12B285020.09
21A281480.07
22C281480.07
31B281400.07
32C281400.07
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 404 -
Rwork0.366 7191 -
obs--99.18 %
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)
13.6061-0.06841.05470.4268-0.07511.9716-0.05970.0066-0.0827-0.01220.00670.0877-0.0435-0.14120.05290.21390.0265-0.03510.6206-0.00920.0289-23.012-40.39651.241
21.9958-0.5211.81340.7756-1.3085.1186-0.15120.04390.16660.0258-0.0077-0.1111-0.65820.31750.15890.3708-0.0283-0.06560.54030.00470.0471-39.23-23.88419.546
32.05271.10310.92312.0721.56324.5320.0007-0.03410.1572-0.22010.0270.0272-0.4280.03-0.02780.25810.0106-0.02690.5349-0.01760.0233-59.588-48.52515.922
41.44080.14111.52991.26251.00846.76450.1022-0.2012-0.12970.1838-0.04830.02430.3187-0.4678-0.0540.22-0.0259-0.03220.4807-0.00870.0525-53.97-46.12554.861
52.5576-0.86991.7671.5213-0.26144.43560.1320.0004-0.22440.0340.10680.11870.20760.1566-0.23890.2985-0.0035-0.09390.5653-0.03580.0507-28.965-40.871-13.716
61.9169-0.06871.66530.8046-0.4514.74060.0685-0.0466-0.0233-0.1144-0.0616-0.04730.09660.1335-0.0070.21230.021-0.02250.6207-0.02060.0082-4.737-44.09417.706
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 177
2X-RAY DIFFRACTION2A178 - 302
3X-RAY DIFFRACTION3B39 - 177
4X-RAY DIFFRACTION4B178 - 302
5X-RAY DIFFRACTION5C39 - 177
6X-RAY DIFFRACTION6C178 - 302

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