5KZT

Listeria monocytogenes OppA bound to peptide

• PDB DOI: https://doi.org/10.2210/pdb5KZT/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Listeria monocytogenes 10403S, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-25 Released: 2016-08-10 
• Deposition Author(s): Light, S.H., Whiteley, A.T., Minasov, G., Portnoy, D.A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.205 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

Listeria monocytogenes OppA bound to peptide

Light, S.H., Whiteley, A.T., Minasov, G., Portnoy, D.A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 122.6 kDa 
• Atom Count: 9,391 
• Modelled Residue Count: 1,031 
• Deposited Residue Count: 1,084 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide/nickel transport system substrate-binding protein	A, B	536	Listeria monocytogenes 10403S	Mutation(s): 0  Gene Names: LMRG_01636
UniProt
Find proteins for A0A0H3GJB6 (Listeria monocytogenes serotype 1/2a (strain 10403S)) Explore A0A0H3GJB6  Go to UniProtKB:  A0A0H3GJB6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexamer peptide: SER-ASP-GLU-SER-LYS-GLY	C	6	Escherichia coli	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexamer peptide: SER-ASP-GLU-SER-SER-GLY	D	6	Escherichia coli	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.205 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/m35kzt

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.277	α = 90
b = 74.63	β = 109.38
c = 155.061	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Light, S.H., Whiteley, A.T., Minasov, G., Portnoy, D.A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description