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- PDB-5y9g: Crystal structure of Salmonella SafD adhesin -

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Basic information

Entry
Database: PDB / ID: 5y9g
TitleCrystal structure of Salmonella SafD adhesin
ComponentsPilin structural protein SafD,Pilus assembly protein
KeywordsCELL ADHESION / host recognition / biofilm formation / Salmonella atypical fimbriae / poly-adhesive activity / self-associating oligomerization
Function / homology: / :
Function and homology information
Biological speciesSalmonella enteritidis (bacteria)
Salmonella choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZeng, L.H. / Zhang, L. / Wang, P.R. / Meng, G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81770142, 81570120 China
National Natural Science Foundation of China81370620, 31070645 China
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: Pilin structural protein SafD,Pilus assembly protein
B: Pilin structural protein SafD,Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)32,5702
Polymers32,5702
Non-polymers00
Water2,252125
1
A: Pilin structural protein SafD,Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)16,2851
Polymers16,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pilin structural protein SafD,Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)16,2851
Polymers16,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.300, 49.710, 148.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pilin structural protein SafD,Pilus assembly protein


Mass: 16284.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enteritidis (bacteria), (gene. exp.) Salmonella choleraesuis (bacteria)
Gene: R567_09630, IN36_14140 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1X2WLP6, UniProt: A0A158MX89
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the sequence DNKQ is an artificial linker.

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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: 1.83 Å3/Da / Density % sol: 32.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→74.4 Å / Num. obs: 11971 / % possible obs: 98 % / Redundancy: 4 % / Rmerge(I) obs: 0.195 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.679 / CC1/2: 0.52 / % possible all: 88.5

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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

2ixq


Resolution: 2.2→47.15 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.52
RfactorNum. reflection% reflection
Rfree0.2326 588 5.07 %
Rwork0.1989 --
obs0.2006 11606 90.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 0 125 2255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032178
X-RAY DIFFRACTIONf_angle_d0.6662963
X-RAY DIFFRACTIONf_dihedral_angle_d14.6641263
X-RAY DIFFRACTIONf_chiral_restr0.048325
X-RAY DIFFRACTIONf_plane_restr0.004391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.42150.33061330.25692624X-RAY DIFFRACTION88
2.4215-2.77180.27681430.23062604X-RAY DIFFRACTION87
2.7718-3.4920.22071400.19652732X-RAY DIFFRACTION90
3.492-100.19561720.16853058X-RAY DIFFRACTION96
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)
12.429-2.225-0.56363.93071.0528.64870.13640.5394-0.48650.02260.0141.19261.1372-1.68290.1134-0.01760.21450.00210.12580.01930.511220.211521.084714.4812
25.2071-1.5792-0.76285.96250.93836.1975-0.0275-0.6875-0.25430.5202-0.11990.00930.3098-0.19330.04380.2794-0.09-0.03670.21380.00330.179635.419441.495819.3521
32.0701-0.04340.57031.11330.39083.38260.1475-0.3094-0.3596-0.0811-0.1294-0.36860.32170.06750.00670.22360.01630.02710.08570.05470.053528.861826.328514.9865
43.07381.4734-0.56715.2925-0.55921.36670.11570.70740.2183-0.46850.1230.10170.1746-0.18030.07370.43870.0111-0.12990.1569-0.08260.125924.975426.00582.8367
53.7444-2.4413-1.22046.67971.56952.0723-0.3893-0.24960.42840.30870.20250.1938-0.37280.10840.12380.2619-0.0234-0.07820.16160.0120.230226.816642.9259.2636
65.68162.09113.50287.2178-0.33692.9233-0.00540.58520.0705-0.8833-0.2049-0.26210.05840.5050.03570.31420.06320.01820.25170.01050.155531.003725.8331-0.2165
74.7092-0.2040.07265.0517-1.02721.39270.25180.8808-0.7474-1.3377-0.3299-0.13621.07780.3420.16040.4410.0924-0.02710.1480.05440.221629.740816.69754.2634
82.59560.34411.24473.64970.43051.9866-0.1729-0.01880.3492-0.12850.0580.3456-0.09770.04220.1170.15060.00920.01440.14910.02390.152128.253535.49811.4667
92.8989-1.5654-1.7953.43350.4643.69340.30740.47410.10280.1265-0.70511.3794-0.0727-1.0767-0.01510.32340.10110.00820.52340.03990.386120.567232.053113.7203
102.88030.99340.21223.56620.27822.2848-0.0989-0.20960.249-0.143-0.07110.2283-0.21190.04550.12430.09630.00640.01730.13380.0160.089336.023126.921324.4617
112.47040.3132-2.76361.8953-1.17783.5786-0.064-0.8264-0.3861-0.00580.37790.02020.49980.7650.04510.13580.04290.00830.22520.04480.22546.002215.933129.268
123.85023.0793-4.47025.5599-3.10037.4676-0.58270.2979-0.6925-0.18810.0932-0.60140.5342-0.47190.23010.13810.06810.01540.21970.0090.14636.255811.188728.4666
133.20041.27080.54673.76511.02211.75090.0366-0.0970.2176-0.21910.0035-0.158-0.24870.0521-0.00610.11990.00510.03490.14940.03630.130146.087328.050222.867
141.52511.2952-0.59885.51061.0542.0306-0.0198-0.16980.12460.2390.0922-0.1209-0.07220.29660.0230.14430.0461-0.04520.175-0.00770.124336.961222.393629.7671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 82 )
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 101 )
6X-RAY DIFFRACTION6chain 'A' and (resid 102 through 114 )
7X-RAY DIFFRACTION7chain 'A' and (resid 115 through 122 )
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 149 )
9X-RAY DIFFRACTION9chain 'A' and (resid 150 through 178 )
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 82 )
12X-RAY DIFFRACTION12chain 'B' and (resid 83 through 101 )
13X-RAY DIFFRACTION13chain 'B' and (resid 102 through 130 )
14X-RAY DIFFRACTION14chain 'B' and (resid 131 through 178 )

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