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- PDB-5hbb: Crystal structure of shaft pilin spaA from Lactobacillus rhamnosu... -

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Basic information

Entry
Database: PDB / ID: 5hbb
TitleCrystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG - E139A 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
THIOCYANATE ION / Cell surface protein SpaA
Similarity search - Component
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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 31, 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_conn_type / 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_conn_type.id / _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 1.2Oct 23, 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
B: Cell surface protein SpaA
A: Cell surface protein SpaA
C: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,74826
Polymers91,9963
Non-polymers75123
Water5,152286
1
B: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9249
Polymers30,6651
Non-polymers2588
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-25 kcal/mol
Surface area13570 Å2
MethodPISA
2
A: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9249
Polymers30,6651
Non-polymers2588
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-25 kcal/mol
Surface area13730 Å2
MethodPISA
3
C: Cell surface protein SpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9018
Polymers30,6651
Non-polymers2357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-25 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.950, 63.488, 104.453
Angle α, β, γ (deg.)90.00, 94.99, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13A
23C

NCS domain segments:

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

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11BA39 - 30112 - 274
21AB39 - 30112 - 274
12BA39 - 30112 - 274
22CC39 - 30112 - 274
13AB38 - 30111 - 274
23CC38 - 30111 - 274

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Cell surface protein SpaA


Mass: 30665.463 Da / Num. of mol.: 3 / Fragment: UNP residues 35-302 / Mutation: E139A
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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 286 / 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: 4.03 Å3/Da / Density % sol: 69.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium thiocynate, 15% PEG3350

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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: Sep 24, 2015
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.47→111.8 Å / Num. obs: 44441 / % possible obs: 83.53 % / Redundancy: 5 % / Rmerge(I) obs: 0.08946 / Rsym value: 0.09943 / Net I/σ(I): 17.36
Reflection shellResolution: 2.466→2.554 Å / Redundancy: 4 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.84 / % possible all: 27.02

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F44

5f44


Resolution: 2.47→111.8 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.887 / SU B: 13.007 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 2240 5 %RANDOM
Rwork0.20045 ---
obs0.2013 42201 83.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.418 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20.56 Å2
2---3.21 Å20 Å2
3---2.02 Å2
Refinement stepCycle: 1 / Resolution: 2.47→111.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6049 0 38 286 6373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026196
X-RAY DIFFRACTIONr_bond_other_d0.0030.025642
X-RAY DIFFRACTIONr_angle_refined_deg1.11.9388422
X-RAY DIFFRACTIONr_angle_other_deg0.853313019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.88925.62274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4815948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6321515
X-RAY DIFFRACTIONr_chiral_restr0.060.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027163
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021390
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_it3.2450.3423184
X-RAY DIFFRACTIONr_mcbond_other3.2110.343180
X-RAY DIFFRACTIONr_mcangle_it3.4890.5023971
X-RAY DIFFRACTIONr_mcangle_other3.4910.5043972
X-RAY DIFFRACTIONr_scbond_it6.6990.5933012
X-RAY DIFFRACTIONr_scbond_other6.6990.5933012
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3960.7434452
X-RAY DIFFRACTIONr_long_range_B_refined8.2173.0876883
X-RAY DIFFRACTIONr_long_range_B_other8.2173.0916884
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)
11B144600.07
12A144600.07
21B144990.07
22C144990.07
31A143700.08
32C143700.08
LS refinement shellResolution: 2.465→2.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 43 -
Rwork0.279 863 -
obs--22.87 %
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)
14.2005-0.1931.65020.40260.04732.532-0.13460.0636-0.07270.05390.04980.0573-0.05380.0670.08480.01190.02780.00590.3509-0.02420.0166-22.229-39.39450.689
21.7947-0.51621.19561.1605-1.8055.0405-0.02490.04810.21080.0591-0.0242-0.0658-0.60110.31060.04910.1961-0.0381-0.01830.2965-0.01490.0504-38.33-22.51219.184
31.7016-0.95181.22091.8933-1.68334.6979-0.0203-0.02760.08680.1590.05070.0072-0.2503-0.0012-0.03030.0384-0.03160.00050.2720.02740.0113-54.406-15.757-16.163
41.87170.0330.9531.8986-0.96435.64350.07930.1636-0.1647-0.3949-0.015-0.15180.35430.2938-0.06430.10090.00680.01670.21560.00450.0312-59.799-13.442-54.923
52.24790.82811.15091.28790.45265.44480.17110.0847-0.28160.03390.0841-0.09230.3497-0.2919-0.25520.2273-0.0347-0.09580.32110.05650.070319.006-40.178117.156
61.69060.12341.79191.1120.60264.96740.0851-0.0017-0.06250.2211-0.08760.09320.1205-0.12030.00250.0633-0.0240.0070.46560.02270.0373-5.039-43.10586.232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 177
2X-RAY DIFFRACTION2A178 - 302
3X-RAY DIFFRACTION3B39 - 177
4X-RAY DIFFRACTION4B178 - 302
5X-RAY DIFFRACTION5C38 - 177
6X-RAY DIFFRACTION6C178 - 302

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