5NBG | pdb_00005nbg

Structure of the cytoplasmic domain I of OutF in the D. dadantii type II secretion system

• PDB DOI: https://doi.org/10.2210/pdb5NBG/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Dickeya dadantii 3937
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-01 Released: 2018-03-21 
• Deposition Author(s): Zhang, H., Gu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Structure of the first cytoplasmic domain of OutF and assembly of the inner-membrane platform proteins of the D. dadantii type II secretion system

Zhang, H., Gu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 23.33 kDa 
• Atom Count: 1,652 
• Modeled Residue Count: 214 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General secretion pathway protein F	A, B	109	Dickeya dadantii 3937	Mutation(s): 0  Gene Names: outF, Dda3937_02417
UniProt
Find proteins for E0SM39 (Dickeya dadantii (strain 3937)) Explore E0SM39  Go to UniProtKB:  E0SM39

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.175	α = 90
b = 116.175	β = 90
c = 47.998	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOLREP	phasing
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Zhang, H., Gu, S.

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description