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- PDB-5z24: Crystal structure of shaft pilin spaD from Lactobacillus rhamnosu... -

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Basic information

Entry
Database: PDB / ID: 5z24
TitleCrystal structure of shaft pilin spaD from Lactobacillus rhamnosus GG - K365A mutant
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionDec 28, 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 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)101,9652
Polymers101,9652
Non-polymers00
Water3,945219
1
A: Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)50,9831
Polymers50,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)50,9831
Polymers50,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.821, 74.886, 403.652
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: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 37 - 480 / Label seq-ID: 9 - 452

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

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Components

#1: Protein Pilus assembly protein / spaD shaft pilin


Mass: 50982.629 Da / Num. of mol.: 2 / Mutation: K365A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus GG (bacteria) / 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.: 219 / Source method: isolated from a natural source / Formula: H2O

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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: 3.84 Å3/Da / Density meas: 1536211.375 Mg/m3 / Density % sol: 67.99 % / Description: Three dimensional plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Magnesium acetate, 0.1M HEPES pH 7.5, 15% 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: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.4→201.83 Å / Num. obs: 35611 / % possible obs: 91.5 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Net I/σ(I): 21.2
Reflection shellResolution: 2.4→2.56 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1782 / CC1/2: 0.958 / Rpim(I) all: 0.283 / Rrim(I) all: 0.478 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YU5

5yu5


Resolution: 2.4→201.83 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.873 / SU B: 21.906 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.737 / ESU R Free: 0.365 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27558 1775 5 %RANDOM
Rwork0.24073 ---
obs0.24245 33837 57.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 50.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2---2.69 Å20 Å2
3---3.46 Å2
Refinement stepCycle: 1 / Resolution: 2.4→201.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 0 219 6878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196789
X-RAY DIFFRACTIONr_bond_other_d0.0010.026119
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9459238
X-RAY DIFFRACTIONr_angle_other_deg0.888314229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3935867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36625.574305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.369151083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7381522
X-RAY DIFFRACTIONr_chiral_restr0.0730.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021290
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_it1.0151.5533483
X-RAY DIFFRACTIONr_mcbond_other1.0151.5543482
X-RAY DIFFRACTIONr_mcangle_it1.8092.3294345
X-RAY DIFFRACTIONr_mcangle_other1.8092.3294346
X-RAY DIFFRACTIONr_scbond_it0.8181.5833306
X-RAY DIFFRACTIONr_scbond_other0.8181.5833307
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4012.354894
X-RAY DIFFRACTIONr_long_range_B_refined4.19718.3016806
X-RAY DIFFRACTIONr_long_range_B_other4.12318.2566792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24862 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 30 -
Rwork0.364 607 -
obs--14.23 %
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)
11.93620.15610.83171.3063-0.45785.63460.0469-0.01910.0348-0.3443-0.15350.32850.1034-0.42030.10670.20220.0841-0.05940.2791-0.04910.1009-34.5921.558-14.932
21.54830.45970.38232.1965-0.88175.13650.01170.1421-0.0017-0.023-0.2706-0.3416-0.12970.29750.25890.0397-0.03030.02180.25120.07280.0794-16.145-1.80810.72
30.629-1.0460.88781.9084-1.57363.179-0.13260.0116-0.04340.4338-0.04010.1471-0.001-0.12620.17260.4749-0.28380.12680.43110.00790.0812-22.189-14.33146.198
41.09121.6732-0.48712.7744-0.07636.0446-0.1199-0.10040.07880.15210.02610.20960.45740.71550.09380.6870.33270.16650.41950.08480.0515-20.0415.018117.813
50.9749-0.46910.09040.8225-0.0594.416-0.1132-0.23550.1540.05620.2101-0.2489-0.96731.3464-0.09681.0498-0.37410.12290.8992-0.01860.1194-5.59232.05895.014
60.39580.2307-0.83181.6795-2.10343.830.0371-0.0345-0.03450.1504-0.11890.04650.15230.34030.08180.6401-0.18830.09230.46980.0140.0229-9.80235.58556.201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 184
2X-RAY DIFFRACTION2A185 - 348
3X-RAY DIFFRACTION3A349 - 480
4X-RAY DIFFRACTION4B36 - 184
5X-RAY DIFFRACTION5B185 - 348
6X-RAY DIFFRACTION6B349 - 485

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