5LZ0 | pdb_00005lz0

Llama nanobody PorM_01

• PDB DOI: https://doi.org/10.2210/pdb5LZ0/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-29 Released: 2017-05-03 
• Deposition Author(s): Duhoo, Y., Leone, P., Roussel, A.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.232 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Camelid nanobodies used as crystallization chaperones for different constructs of PorM, a component of the type IX secretion system from Porphyromonas gingivalis.

Duhoo, Y., Roche, J., Trinh, T.T.N., Desmyter, A., Gaubert, A., Kellenberger, C., Cambillau, C., Roussel, A., Leone, P.

(2017) Acta Crystallogr F Struct Biol Commun 73: 286-293

• PubMed: 28471361 
• DOI: https://doi.org/10.1107/S2053230X17005969
• Primary Citation Related Structures: 
  5FWO, 5LMJ, 5LMW, 5LZ0


• PubMed Abstract: 
  

  PorM is a membrane protein that is involved in the assembly of the type IX secretion system (T9SS) in Porphyromonas gingivalis, a major bacterial pathogen that is responsible for periodontal disease in humans. In the context of structural studies of PorM to better understand T9SS assembly, four camelid nanobodies were selected, produced and purified, and their specific interaction with the N-terminal or C-terminal part of the periplasmic domain of PorM was investigated. Diffracting crystals were also obtained, and the structures of the four nanobodies were solved by molecular replacement. Furthermore, two nanobodies were used as crystallization chaperones and turned out to be valuable tools in the structure-determination process of the periplasmic domain of PorM.

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Organizational Affiliation: 
• Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.99 kDa 
• Atom Count: 2,153 
• Modeled Residue Count: 247 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PorM nanobody	A, B	134	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.232 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.327	α = 90
b = 65.828	β = 95.89
c = 48.314	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Duhoo, Y., Leone, P., Roussel, A.

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Funding Organization	Location	Grant Number
French National Research Agency	France	--

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references
• Version 1.2: 2017-05-17
  Changes: Database references
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence
• Version 1.4: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary