9RMM | pdb_00009rmm

Crystal structure of outer membrane SilC

PDB DOI: https://doi.org/10.2210/pdb9RMM/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-06-18 Released: 2025-07-23
Deposition Author(s): Lithgo, R.M., Carr, S.B., Quigley, A.M., Scott, D.J.
Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.284 (Depositor), 0.284 (DCC)
R-Value Work:
0.237 (Depositor), 0.237 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Structural characterisation of the outer membrane protein SilC, involved in bacterial silver resistance.

Lithgo, R.M., Carr, S.B., Quigley, A.M., Scott, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 307.91 kDa
Atom Count: 20,536
Modeled Residue Count: 2,620
Deposited Residue Count: 2,773
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable outer membrane lipoprotein SilC	A, B, D, E, F	462	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: silC
UniProt
Find proteins for Q9ZHD2 (Salmonella typhimurium) Explore Q9ZHD2 Go to UniProtKB: Q9ZHD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZHD2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable outer membrane lipoprotein SilC	C	463	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: silC
UniProt
Find proteins for Q9ZHD2 (Salmonella typhimurium) Explore Q9ZHD2 Go to UniProtKB: Q9ZHD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZHD2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.284 (Depositor), 0.284 (DCC)
R-Value Work: 0.237 (Depositor), 0.237 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.055	α = 90
b = 326.789	β = 120.27
c = 88.101	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	202892/Z/16/Z
Wellcome Trust	United Kingdom	223727/Z/21/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M008770/1

Revision History (Full details and data files)

Version 1.0: 2025-07-23
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.