4WFW | pdb_00004wfw

The crystal structure of Dickeya dadantii GspB from the type 2 secretion system

• PDB DOI: https://doi.org/10.2210/pdb4WFW/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Dickeya dadantii 3937
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-17 Released: 2015-09-30 
• Deposition Author(s): Rycroft, P.B., Pickersgill, R.W., Shevchik, V.E.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of Dickeya dadantii GspB from the type 2 secretion system

Rycroft, P.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 9.92 kDa 
• Atom Count: 676 
• Modeled Residue Count: 84 
• Deposited Residue Count: 90 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General secretion pathway protein B	A	90	Dickeya dadantii 3937	Mutation(s): 0  Gene Names: outB, Dda3937_02412
UniProt
Find proteins for Q01563 (Dickeya dadantii (strain 3937)) Explore Q01563  Go to UniProtKB:  Q01563

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.21	α = 90
b = 36.21	β = 90
c = 131.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Rycroft, P.B., Pickersgill, R.W., Shevchik, V.E.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/I013334/1

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 2.0: 2017-08-30
  Changes: Advisory, Atomic model, Author supporting evidence
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description