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- PDB-6m48: Crystal structure of pilus adhesin, SpaC from Lactobacillus rhamn... -

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Basic information

Entry
Database: PDB / ID: 6m48
TitleCrystal structure of pilus adhesin, SpaC from Lactobacillus rhamnosus GG - P21212 form
ComponentsSpaCSpecial-purpose acquisition company
KeywordsCELL ADHESION / Pilus adhesin / Tip pilin / vWFA domain / SpaCBA pilus / sortase / Lactobacillus rhamnosus GG / pili / fimbria / Probiotics / SpaC / lectin / surface protein / MIDAS
Function / homologyPrealbumin-like fold domain / Prealbumin-like fold domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold / Pilus assembly protein
Function and homology information
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKant, A. / Palva, A. / Von Ossowaski, I. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PRS891/BRB/10/1098/20 India
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Crystal structure of lactobacillar SpaC reveals an atypical five-domain pilus tip adhesin: Exposing its substrate-binding and assembly in SpaCBA pili.
Authors: Kant, A. / Palva, A. / von Ossowski, I. / Krishnan, V.
History
DepositionMar 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Sep 15, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SpaC
B: SpaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,9926
Polymers181,8732
Non-polymers1204
Water5,459303
1
A: SpaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0324
Polymers90,9361
Non-polymers953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area35950 Å2
MethodPISA
2
B: SpaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9612
Polymers90,9361
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area36620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.181, 128.128, 136.358
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

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 38 - 852 / Label seq-ID: 10 - 824

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein SpaC / Special-purpose acquisition company


Mass: 90936.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus GG (bacteria) / Gene: LGG_00444 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A1Y0DVK9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 0.25M Sodium sulphate, 0.1M BIS-Tris propane pH 6.5, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.5→46.69 Å / Num. obs: 70856 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.057 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4503 / CC1/2: 0.718 / Rpim(I) all: 0.631

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M3Y
Resolution: 2.5→44.26 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 19.094 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.259 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23525 3635 5.1 %RANDOM
Rwork0.19168 ---
obs0.19393 67165 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0 Å2
2---1.91 Å20 Å2
3---1.65 Å2
Refinement stepCycle: 1 / Resolution: 2.5→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12201 0 4 303 12508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01312465
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710730
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.64816962
X-RAY DIFFRACTIONr_angle_other_deg1.321.57225042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.66251619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14325.35600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.591151902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1681532
X-RAY DIFFRACTIONr_chiral_restr0.0690.21720
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022377
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_it3.8325.076495
X-RAY DIFFRACTIONr_mcbond_other3.8325.076494
X-RAY DIFFRACTIONr_mcangle_it5.8657.5958107
X-RAY DIFFRACTIONr_mcangle_other5.8647.5968108
X-RAY DIFFRACTIONr_scbond_it4.3235.2235970
X-RAY DIFFRACTIONr_scbond_other4.3155.2245966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7037.7068856
X-RAY DIFFRACTIONr_long_range_B_refined10.20493.78251879
X-RAY DIFFRACTIONr_long_range_B_other10.20693.80151767
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23310 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 276 -
Rwork0.28 4917 -
obs--99.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.22730.19840.02641.1172-0.50530.63290.0270.0914-0.02740.0157-0.01240.00260.02860.0557-0.01460.10180.03360.00140.0513-0.00810.076532.219245.29952.646
20.39-0.37290.09781.18990.10280.40410.00660.02420.04160.0007-0.0442-0.02460.0238-0.04230.03770.09320.0011-0.00030.0249-0.01220.117742.138199.57860.561
30.50780.1036-0.41694.26052.13851.5109-0.0520.0515-0.08880.19370.0015-0.08360.1395-0.05220.05050.16840.0244-0.04510.0176-0.0360.07950.113161.23145.248
41.4508-0.7460.06321.8257-0.44550.4030.16010.1384-0.1354-0.1098-0.05350.2848-0.09590.091-0.10660.08620.0004-0.02510.0603-0.03520.139445.63134.79721.767
50.16920.5180.20295.10080.43780.41680.124-0.09590.04410.604-0.3847-0.57450.0232-0.06160.26070.1853-0.1061-0.12810.07420.04630.332645.60692.68115.758
60.12250.3132-0.03661.0010.02020.6341-0.038-0.0167-0.04560.0161-0.0038-0.06580.05990.00130.04170.12240.01150.05850.01720.01740.133932.83951.51815.761
70.61260.2736-0.18941.5889-0.38640.85330.0368-0.08170.0416-0.0224-0.0677-0.0463-0.01960.05770.0310.06430.00070.00570.0352-0.00030.103316.7976.83911.398
80.1180.5418-0.28323.1554-1.02420.90870.0213-0.0060.00240.0102-0.08450.03970.00760.02240.06320.11870.0054-0.00740.04450.06980.135510.628-32.24727.096
90.96490.0987-0.16251.363-0.10261.5478-0.0093-0.14410.0457-0.07650.04780.06260.17040.0165-0.03840.09070.0139-0.0010.03850.02310.071714.675-60.70147.727
100.8977-0.541-0.22463.6205-0.46680.90040.36860.1357-0.0507-0.182-0.41520.1890.0533-0.17920.04650.2684-0.016-0.09040.1193-0.01670.10025.326-101.53347.886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B129 - 385
2X-RAY DIFFRACTION2B37 - 128
3X-RAY DIFFRACTION2B386 - 493
4X-RAY DIFFRACTION3B494 - 597
5X-RAY DIFFRACTION4B598 - 731
6X-RAY DIFFRACTION5B732 - 857
7X-RAY DIFFRACTION6A129 - 385
8X-RAY DIFFRACTION7A38 - 128
9X-RAY DIFFRACTION7A386 - 493
10X-RAY DIFFRACTION8A494 - 597
11X-RAY DIFFRACTION9A598 - 731
12X-RAY DIFFRACTION10A732 - 852

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