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- PDB-5y9h: Crystal structure of SafDAA-dsc complex -

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Basic information

Entry
Database: PDB / ID: 5y9h
TitleCrystal structure of SafDAA-dsc complex
ComponentsSafD,Putative outer membrane protein,Putative outer membrane protein,Putative outer membrane protein
KeywordsCELL ADHESION / host recognition / biofilm formation / Salmonella atypical fimbriae / poly-adhesive activity / self-associating oligomerization
Function / homology
Function and homology information


Enterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Saf-pilin pilus formation protein / Saf-pilin pilus formation protein / Dr-adhesin superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Enterobacteria AfaD invasin protein / Putative fimbriae subunit / Outer membrane protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZeng, L.H. / Zhang, L. / Wang, P.R. / Meng, G.
CitationJournal: Elife / Year: 2017
Title: Structural basis of host recognition and biofilm formation by Salmonella Saf pili
Authors: Zeng, L.H. / Zhang, L. / Wang, P.R. / Meng, G.
History
DepositionAug 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SafD,Putative outer membrane protein,Putative outer membrane protein,Putative outer membrane protein
B: SafD,Putative outer membrane protein,Putative outer membrane protein,Putative outer membrane protein
C: SafD,Putative outer membrane protein,Putative outer membrane protein,Putative outer membrane protein


Theoretical massNumber of molelcules
Total (without water)150,1933
Polymers150,1933
Non-polymers00
Water90150
1
A: SafD,Putative outer membrane protein,Putative outer membrane protein,Putative outer membrane protein


Theoretical massNumber of molelcules
Total (without water)50,0641
Polymers50,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SafD,Putative outer membrane protein,Putative outer membrane protein,Putative outer membrane protein


Theoretical massNumber of molelcules
Total (without water)50,0641
Polymers50,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SafD,Putative outer membrane protein,Putative outer membrane protein,Putative outer membrane protein


Theoretical massNumber of molelcules
Total (without water)50,0641
Polymers50,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.270, 66.070, 187.680
Angle α, β, γ (deg.)90.00, 96.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SafD,Putative outer membrane protein,Putative outer membrane protein,Putative outer membrane protein / Salmonella atypical fimbria subunit D (SafD)


Mass: 50064.305 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: safD, safA, STM0299 / Strain: LT2 / SGSC1412 / ATCC 700720 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: H9L4M7, UniProt: Q8ZRK4, UniProt: Q7CR56*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→93.3 Å / Num. obs: 38710 / % possible obs: 96 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6 % / Rmerge(I) obs: 1.48 / CC1/2: 0.44 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IXQ and 5Y9G

2ixq

5y9g


Resolution: 2.8→93.288 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.33
RfactorNum. reflection% reflection
Rfree0.2548 1894 4.9 %
Rwork0.2188 --
obs0.2205 38663 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→93.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9543 0 0 50 9593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069675
X-RAY DIFFRACTIONf_angle_d0.99313178
X-RAY DIFFRACTIONf_dihedral_angle_d16.9215723
X-RAY DIFFRACTIONf_chiral_restr0.0591550
X-RAY DIFFRACTIONf_plane_restr0.0051715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.39491530.36322629X-RAY DIFFRACTION96
2.87-2.94760.38481200.36482567X-RAY DIFFRACTION96
2.9476-3.03440.41131250.34092620X-RAY DIFFRACTION95
3.0344-3.13230.32511090.31752641X-RAY DIFFRACTION96
3.1323-3.24430.34881530.28732580X-RAY DIFFRACTION95
3.2443-3.37420.30491390.27342589X-RAY DIFFRACTION95
3.3742-3.52780.2731460.26262583X-RAY DIFFRACTION95
3.5278-3.71380.28131160.2412602X-RAY DIFFRACTION95
3.7138-3.94640.23031340.21692614X-RAY DIFFRACTION96
3.9464-4.25110.22971370.18972586X-RAY DIFFRACTION95
4.2511-4.67890.20111460.17452607X-RAY DIFFRACTION95
4.6789-5.35590.17661450.16222655X-RAY DIFFRACTION96
5.3559-6.74760.26181270.19972679X-RAY DIFFRACTION96
6.7476-93.33940.25071440.18752817X-RAY DIFFRACTION99
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)
15.86620.01762.16842.36080.78395.8043-0.4393-0.2411.35840.0758-0.17790.1315-0.4876-0.49540.5310.70990.2116-0.01730.4153-0.0590.912-17.8131-11.9824-4.7781
25.3853-0.6682.75691.3036-0.42215.26880.1534-1.0712-0.04070.0171-0.0723-0.0760.0498-0.559-0.05870.3491-0.05370.0910.45710.00540.40558.4928-30.048522.5977
36.9774-0.02440.41115.3353-1.25836.26610.2099-0.84490.2840.3423-0.0454-0.2143-0.0897-0.8459-0.11360.5392-0.07230.03360.7274-0.11820.442941.4475-33.350354.2462
43.88470.04822.40272.7097-0.12653.8939-0.31770.07070.92430.6224-0.3581-0.2407-0.35410.33770.58840.7692-0.2064-0.0870.69440.2280.794.17828.430950.1316
50.10341.13912.0443-0.61822.14953.74190.05850.4632-0.02730.05960.24290.07310.57380.5116-0.23531.94240.1285-0.5051.3213-0.21581.064333.384412.2384105.4595
63.17371.83081.01974.55731.48912.16150.10791.0315-0.1980.5439-0.0462-1.6020.31042.2756-0.01760.8083-0.0582-0.15381.87540.34141.28426.2903-4.714548.5069
78.57030.48372.26254.44730.3685.00220.61510.0962-0.55630.2333-0.32130.17180.46890.2321-0.25410.56010.0380.01090.3734-0.04190.3004-11.6569-15.274138.0287
81.8679-0.86660.16331.93710.11332.87030.92030.7457-1.05420.3771-0.2405-0.06460.43740.3408-0.43070.48850.09530.02790.60810.03120.5716-12.5172-12.462829.9896
95.41970.3431-0.27554.4951-2.4919.23070.40710.2319-0.7957-0.13380.1061-0.57391.14860.823-0.33790.52690.1224-0.07360.4901-0.16880.6727-45.6317-11.40614.1722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 167 )
2X-RAY DIFFRACTION2chain 'A' and (resid 168 through 328 )
3X-RAY DIFFRACTION3chain 'A' and (resid 329 through 466 )
4X-RAY DIFFRACTION4chain 'B' and (resid 21 through 294 )
5X-RAY DIFFRACTION5chain 'B' and (resid 295 through 465 )
6X-RAY DIFFRACTION6chain 'C' and (resid 23 through 168 )
7X-RAY DIFFRACTION7chain 'C' and (resid 169 through 294 )
8X-RAY DIFFRACTION8chain 'C' and (resid 295 through 328 )
9X-RAY DIFFRACTION9chain 'C' and (resid 329 through 465 )

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