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

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Basic information

Entry
Database: PDB / ID: 5fgr
TitleCrystal structure of C-terminal domain of shaft pilin spaA from Lactobacillus rhamnosus GG - P21212 space group with Yb Heavy atom
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
YTTERBIUM (III) ION / Cell surface protein SpaA
Similarity search - Component
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 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 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.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.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

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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)60,03414
Polymers58,3034
Non-polymers1,73010
Water46826
1
A: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2685
Polymers14,5761
Non-polymers6924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-10 kcal/mol
Surface area6300 Å2
MethodPISA
2
B: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9223
Polymers14,5761
Non-polymers3462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-8 kcal/mol
Surface area6370 Å2
MethodPISA
3
C: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0954
Polymers14,5761
Non-polymers5193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-14 kcal/mol
Surface area6630 Å2
MethodPISA
4
D: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7492
Polymers14,5761
Non-polymers1731
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-9 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.603, 75.252, 117.388
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
11B
21D
12B
22A
13B
23C
14D
24A
15D
25C
16A
26C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRPROPROBB178 - 2972 - 121
21TYRTYRPROPRODD178 - 2972 - 121
12TYRTYRALAALABB178 - 2962 - 120
22TYRTYRALAALAAA178 - 2962 - 120
13TYRTYRPROPROBB178 - 2972 - 121
23TYRTYRPROPROCC178 - 2972 - 121
14THRTHRALAALADD177 - 2961 - 120
24THRTHRALAALAAA177 - 2961 - 120
15THRTHRSERSERDD177 - 2981 - 122
25THRTHRSERSERCC177 - 2981 - 122
16THRTHRALAALAAA177 - 2961 - 120
26THRTHRALAALACC177 - 2961 - 120

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 14575.775 Da / Num. of mol.: 4 / Fragment: C-terminal domain, residues 177-302
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-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Yb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 0.02M zinc sulphate, 25% PEG 550MME, 50mM Yb-DTPA-BMA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.28136 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28136 Å / Relative weight: 1
ReflectionResolution: 2.79→45.74 Å / Num. obs: 13205 / % possible obs: 99.8 % / Redundancy: 14 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.7
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 7.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata processing
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.79→45.74 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 29.621 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23583 650 4.9 %RANDOM
Rwork0.19738 ---
obs0.19916 12523 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.155 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å20 Å2
2--1.99 Å20 Å2
3----5.18 Å2
Refinement stepCycle: 1 / Resolution: 2.79→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 10 26 3719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023747
X-RAY DIFFRACTIONr_bond_other_d0.0030.023358
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.9415066
X-RAY DIFFRACTIONr_angle_other_deg0.75437776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09926.158177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83815602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.619158
X-RAY DIFFRACTIONr_chiral_restr0.0560.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024350
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02826
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_it1.8053.7871940
X-RAY DIFFRACTIONr_mcbond_other1.8053.7871939
X-RAY DIFFRACTIONr_mcangle_it2.9715.6812418
X-RAY DIFFRACTIONr_mcangle_other2.975.6812419
X-RAY DIFFRACTIONr_scbond_it2.4054.0631807
X-RAY DIFFRACTIONr_scbond_other2.4054.0631807
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9685.9722649
X-RAY DIFFRACTIONr_long_range_B_refined6.91430.2084069
X-RAY DIFFRACTIONr_long_range_B_other6.91630.2054066
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)
11B66900.03
12D66900.03
21B65730.04
22A65730.04
31B66420.04
32C66420.04
41D66750.04
42A66750.04
51D67390.04
52C67390.04
61A66110.04
62C66110.04
LS refinement shellResolution: 2.794→2.866 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 46 -
Rwork0.282 873 -
obs--97.04 %
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)
12.69651.23340.14595.14190.01592.16150.0326-0.18870.16130.003-0.03940.0769-0.1073-0.01030.00690.0089-0.0118-0.0230.1741-0.00230.2656-12.134946.397449.1488
22.38360.19810.28788.0884-2.23874.6423-0.25280.18750.108-0.35580.1781-0.29480.2783-0.19130.07470.1393-0.0130.07390.1865-0.00740.0852-14.950731.91379.8796
32.22620.52141.33033.0616-0.69217.71070.02810.1176-0.0933-0.3488-0.0634-0.21870.42230.3760.03530.07390.06870.04290.13320.01710.2147-15.373619.740736.738
43.1047-0.9727-1.68393.07210.81545.92250.16770.20320.2265-0.093-0.0581-0.1314-0.64130.3157-0.10960.1632-0.1119-0.02180.11190.04810.1217-10.858358.829921.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A177 - 297
2X-RAY DIFFRACTION2B178 - 298
3X-RAY DIFFRACTION3C177 - 298
4X-RAY DIFFRACTION4D177 - 298

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