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- PDB-5yxg: Crystal structure of C-terminal fragment of SpaD from Lactobacill... -

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Basic information

Entry
Database: PDB / ID: 5yxg
TitleCrystal structure of C-terminal fragment of SpaD from Lactobacillus rhamnosus GG generated by limited proteolysis
Components(Pilus assembly protein) x 2
KeywordsCELL ADHESION / Pilin / SpaD / probiotic / isopeptide / SpaFED pili / adhesin
Function / homology
Function and homology information


Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pilus assembly protein
Similarity search - Component
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 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 5, 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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: Pilus assembly protein
B: Pilus assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9946
Polymers69,8522
Non-polymers1424
Water14,070781
1
A: Pilus assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9782
Polymers34,9421
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13920 Å2
MethodPISA
2
B: Pilus assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0164
Polymers34,9101
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.106, 83.160, 149.403
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: VAL / Beg label comp-ID: VAL / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 184 - 480 / Label seq-ID: 8 - 304

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

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Components

#1: Protein Pilus assembly protein / spaD


Mass: 34942.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The SME 244 and SME 275 in chain A are radiation induced modification of Methionine
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: Protein Pilus assembly protein


Mass: 34910.055 Da / Num. of mol.: 1
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
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.22 Å3/Da / Density meas: 622534.625 Mg/m3 / Density % sol: 44.71 % / Description: Three dimension rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium chloride 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95371 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 1.48→72.66 Å / Num. obs: 104530 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.029 / Rrim(I) all: 0.07 / Net I/σ(I): 15.6
Reflection shellResolution: 1.48→1.62 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 24710 / CC1/2: 0.813 / Rpim(I) all: 0.253 / Rrim(I) all: 0.596 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: 5YU5

5yu5


Resolution: 1.48→72.66 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.747 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19534 5220 5 %RANDOM
Rwork0.17714 ---
obs0.17807 99221 99.63 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.613 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.48→72.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4581 0 4 781 5366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024710
X-RAY DIFFRACTIONr_bond_other_d0.0010.024306
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9516408
X-RAY DIFFRACTIONr_angle_other_deg0.624310007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9965601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23125.369203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40215767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0841516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025277
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02911
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_it1.0591.3972404
X-RAY DIFFRACTIONr_mcbond_other1.0571.3972403
X-RAY DIFFRACTIONr_mcangle_it1.7012.0893005
X-RAY DIFFRACTIONr_mcangle_other1.7012.0893006
X-RAY DIFFRACTIONr_scbond_it1.7651.6172306
X-RAY DIFFRACTIONr_scbond_other1.7641.6172306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7052.3473403
X-RAY DIFFRACTIONr_long_range_B_refined5.2619.0585289
X-RAY DIFFRACTIONr_long_range_B_other4.90617.6775050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17346 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 395 -
Rwork0.293 7213 -
obs--99.06 %
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)
10.2984-0.17920.22530.1485-0.14360.1963-0.0163-0.00730.02520.0059-0.0126-0.0199-0.0232-0.00770.02890.02570.0107-0.00350.024-0.00020.0061-19.121-8.1178.574
20.32210.31990.09640.33020.10020.03240.0079-0.0005-0.02560.01810.0024-0.03460.0109-0.0066-0.01030.0217-0.0185-0.00540.0335-0.00650.0097-9.228-15.79745.698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A184 - 358
2X-RAY DIFFRACTION1A359 - 481
3X-RAY DIFFRACTION2B177 - 358
4X-RAY DIFFRACTION2B359 - 486

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