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- PDB-5yu5: Crystal structure of shaft pilin spaD from Lactobacillus rhamnosus GG -

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Basic information

Entry
Database: PDB / ID: 5yu5
TitleCrystal structure of shaft pilin spaD from Lactobacillus rhamnosus GG
ComponentsPilus assembly protein
KeywordsCELL ADHESION / Pilin / spaD / probiotic / isopeptide / SpaFED pili / adhesin
Function / homologyGram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / Pilus assembly protein
Function and homology information
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.27 Å
AuthorsChaurasia, P. / Pratap, S. / Palva, A. / von Ossowski, I. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyBT/PR5891/BRB/10/1098/2012 India
CitationJournal: Commun Biol / Year: 2018
Title: Bent conformation of a backbone pilin N-terminal domain supports a three-stage pilus assembly mechanism.
Authors: Chaurasia, P. / Pratap, S. / Palva, A. / von Ossowski, I. / Krishnan, V.
History
DepositionNov 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Pilus assembly protein
B: Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)102,0812
Polymers102,0812
Non-polymers00
Water6,467359
1
A: Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)51,0411
Polymers51,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)51,0411
Polymers51,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.412, 76.264, 400.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 37 - 483 / Label seq-ID: 9 - 455

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

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Components

#1: Protein Pilus assembly protein


Mass: 51040.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus GG / Strain: GG / Gene: CCE29_10230, PY66_09460 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: A0A179XFF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 4.22 Å3/Da / Density % sol: 70.86 % / Description: Three dimensional plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.5, 30% w/v PEG 400

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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: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.27→200 Å / Num. obs: 39269 / % possible obs: 87.1 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.021 / Rrim(I) all: 0.051 / Net I/σ(I): 18.1
Reflection shellResolution: 2.273→2.536 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1964 / CC1/2: 0.93 / Rpim(I) all: 0.236 / Rrim(I) all: 0.533 / % possible all: 48.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.27→200 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.884 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.545 / ESU R Free: 0.303 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23616 1995 5.1 %RANDOM
Rwork0.20173 ---
obs0.20348 37274 50.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 51.045 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2---1.26 Å20 Å2
3---2.17 Å2
Refinement stepCycle: 1 / Resolution: 2.27→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6863 0 0 359 7222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197002
X-RAY DIFFRACTIONr_bond_other_d0.0010.026322
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9439514
X-RAY DIFFRACTIONr_angle_other_deg0.853314720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5925.584317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.372151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4351522
X-RAY DIFFRACTIONr_chiral_restr0.0690.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027839
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021331
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_it1.2792.5343564
X-RAY DIFFRACTIONr_mcbond_other1.2782.5343563
X-RAY DIFFRACTIONr_mcangle_it2.2173.7964448
X-RAY DIFFRACTIONr_mcangle_other2.2173.7964449
X-RAY DIFFRACTIONr_scbond_it1.2692.6583438
X-RAY DIFFRACTIONr_scbond_other1.2682.6583439
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1493.9285067
X-RAY DIFFRACTIONr_long_range_B_refined4.00629.3577147
X-RAY DIFFRACTIONr_long_range_B_other3.98229.3067124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 26694 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.273→2.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 10 -
Rwork0.404 115 -
obs--2.19 %
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)
11.8466-0.26010.09511.30220.88576.5703-0.0559-0.06350.01410.117-0.179-0.2341-0.21370.70550.23480.3155-0.0353-0.12280.41740.07750.093512.0570.36714.738
21.6928-0.3030.0790.71291.2286.32550.044-0.22880.04820.0353-0.23820.1333-0.3432-0.49520.19410.33610.1426-0.07450.2859-0.09330.0903-6.545-2.588-10.358
31.36641.02850.24911.39321.51134.7183-0.0785-0.0265-0.074-0.1035-0.0423-0.0668-0.3302-0.13060.12090.31390.2732-0.05170.2526-0.04360.0254-1.605-14.33-46.583
41.19411.30490.92593.77120.93685.6305-0.0825-0.07760.0261-0.060.06030.06620.0894-0.23260.02220.12750.1069-0.01990.1142-0.01630.004220.93722.291116.816
50.711-0.0191-0.26231.28761.10845.5755-0.1145-0.1476-0.01520.2116-0.15540.31580.237-1.0560.270.27-0.1147-0.01850.3729-0.0350.1248.0444.10994.22
60.18-0.0465-0.02691.10531.07254.4714-0.08180.12090.0623-0.2199-0.11840.1124-0.5039-0.73470.20010.2805-0.0954-0.09220.31980.02070.048812.5460.45755.377
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 184
2X-RAY DIFFRACTION2A185 - 348
3X-RAY DIFFRACTION3A349 - 483
4X-RAY DIFFRACTION4B35 - 184
5X-RAY DIFFRACTION5B185 - 348
6X-RAY DIFFRACTION6B349 - 486

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