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- PDB-9rmm: Crystal structure of outer membrane SilC -

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Basic information

Entry
Database: PDB / ID: 9rmm
TitleCrystal structure of outer membrane SilC
Components(Probable outer membrane lipoprotein SilC) x 2
KeywordsMEMBRANE PROTEIN / SilC / sil / outer membrane / silver resistance / cus / CusC / silver
Function / homologyRND efflux system, outer membrane lipoprotein, NodT / : / Outer membrane efflux protein / Outer membrane efflux protein / efflux transmembrane transporter activity / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Probable outer membrane lipoprotein SilC
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLithgo, R.M. / Carr, S.B. / Quigley, A.M. / Scott, D.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust202892/Z/16/Z United Kingdom
Wellcome Trust223727/Z/21/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M008770/1 United Kingdom
CitationJournal: To Be Published
Title: Structural characterisation of the outer membrane protein SilC, involved in bacterial silver resistance.
Authors: Lithgo, R.M. / Carr, S.B. / Quigley, A.M. / Scott, D.J.
History
DepositionJun 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable outer membrane lipoprotein SilC
B: Probable outer membrane lipoprotein SilC
C: Probable outer membrane lipoprotein SilC
D: Probable outer membrane lipoprotein SilC
E: Probable outer membrane lipoprotein SilC
F: Probable outer membrane lipoprotein SilC


Theoretical massNumber of molelcules
Total (without water)307,9116
Polymers307,9116
Non-polymers00
Water00
1
A: Probable outer membrane lipoprotein SilC
B: Probable outer membrane lipoprotein SilC
C: Probable outer membrane lipoprotein SilC


Theoretical massNumber of molelcules
Total (without water)154,0253
Polymers154,0253
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15740 Å2
ΔGint-94 kcal/mol
Surface area59130 Å2
2
D: Probable outer membrane lipoprotein SilC
E: Probable outer membrane lipoprotein SilC
F: Probable outer membrane lipoprotein SilC


Theoretical massNumber of molelcules
Total (without water)153,8873
Polymers153,8873
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16000 Å2
ΔGint-91 kcal/mol
Surface area59240 Å2
Unit cell
Length a, b, c (Å)88.055, 326.789, 88.101
Angle α, β, γ (deg.)90.000, 120.270, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Probable outer membrane lipoprotein SilC


Mass: 51295.531 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: silC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZHD2
#2: Protein Probable outer membrane lipoprotein SilC


Mass: 51433.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: silC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZHD2
Has protein modificationN

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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: 3.56 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M Sodium Citrate pH 5 0.1M Magnesium Chloride hexahydrate 11% PEG 4000 20% Glycerol (Cryo)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 3.2→44.29 Å / Num. obs: 70140 / % possible obs: 99.35 % / Redundancy: 3.4 % / Biso Wilson estimate: 46.16 Å2 / CC1/2: 0.94 / Net I/σ(I): 3.5
Reflection shellResolution: 3.203→3.317 Å / Num. unique obs: 4668 / CC1/2: 0.418

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→44.29 Å / SU ML: 0.4902 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2837 3469 4.96 %
Rwork0.2367 66441 -
obs0.2391 69910 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.72 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20525 0 0 0 20525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010420874
X-RAY DIFFRACTIONf_angle_d1.184328266
X-RAY DIFFRACTIONf_chiral_restr0.05983152
X-RAY DIFFRACTIONf_plane_restr0.01123758
X-RAY DIFFRACTIONf_dihedral_angle_d5.58722875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.250.39221790.31132566X-RAY DIFFRACTION95.18
3.25-3.290.37311350.31142598X-RAY DIFFRACTION99.74
3.29-3.340.32131120.30322696X-RAY DIFFRACTION99.93
3.34-3.390.30341050.28882756X-RAY DIFFRACTION99.9
3.39-3.450.35181580.29212581X-RAY DIFFRACTION99.93
3.45-3.510.31321170.27822734X-RAY DIFFRACTION99.69
3.51-3.570.30971240.28242634X-RAY DIFFRACTION99.64
3.57-3.640.36381380.28942712X-RAY DIFFRACTION99.62
3.64-3.720.31921670.24252598X-RAY DIFFRACTION99.6
3.72-3.80.3051470.25822654X-RAY DIFFRACTION99.64
3.8-3.880.29391290.2392648X-RAY DIFFRACTION99.96
3.89-3.980.35042050.23192643X-RAY DIFFRACTION99.93
3.98-4.090.25251240.21662639X-RAY DIFFRACTION99.96
4.09-4.210.24681570.21682680X-RAY DIFFRACTION99.68
4.21-4.350.2851370.21622632X-RAY DIFFRACTION99.21
4.35-4.50.21681700.19962613X-RAY DIFFRACTION99.78
4.5-4.680.24861540.20032658X-RAY DIFFRACTION99.68
4.68-4.890.22981250.21732749X-RAY DIFFRACTION99.62
4.89-5.150.2061520.2062608X-RAY DIFFRACTION99.5
5.15-5.470.3299980.22972707X-RAY DIFFRACTION99.54
5.47-5.90.28171580.24292649X-RAY DIFFRACTION99.4
5.9-6.490.29581370.22552628X-RAY DIFFRACTION99.78
6.49-7.420.2459870.21012749X-RAY DIFFRACTION99.93
7.42-9.340.19431520.18252631X-RAY DIFFRACTION98.58
8-44.290.29971020.21462678X-RAY DIFFRACTION97.3

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