2W8H | pdb_00002w8h

Crystal structure of spin labeled Wza24-345.

• PDB DOI: https://doi.org/10.2210/pdb2W8H/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2009-01-16 Released: 2009-02-10 
• Deposition Author(s): Hagelueken, G., Ingledew, W.J., Huang, H., Petrovic-Stojanovska, B., Whitfield, C., ElMkami, H., Schiemann, O., Naismith, J.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.229 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Peldor Distance Fingerprinting of the Octameric Outer-Membrane Protein Wza from Escherichia Coli.

Hagelueken, G., Ingledew, W.J., Huang, H., Petrovic-Stojanovska, B., Whitfield, C., Elmkami, H., Schiemann, O., Naismith, J.H.

(2009) Angew Chem Int Ed Engl 48: 2904

• PubMed: 19294709 
• DOI: https://doi.org/10.1002/anie.200805758
• Primary Citation of Related Structures:  
  2W8H, 2W8I


• PubMed Abstract: 
  

  Distance fingerprinting: Pulsed electron-electron double resonance spectroscopy (PELDOR) is applied to the octameric membrane protein complex Wza of E. coli. The data yielded a detailed distance fingerprint of its periplasmic region that compares favorably to the crystal structure. These results provide the foundation to study conformation changes from interaction with partner proteins.

---

Organizational Affiliation: 

Centre for Biomolecular Sciences, The University of St. Andrews, Fife KY16 9RH, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C8  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 289.08 kDa 
• Atom Count: 19,998 
• Modelled Residue Count: 2,576 
• Deposited Residue Count: 2,632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA	A, B, C, D, E, F, G, H	329	Escherichia coli	Mutation(s): 1  Membrane Entity: Yes
UniProt
Find proteins for Q9X4B7 (Escherichia coli) Explore Q9X4B7  Go to UniProtKB:  Q9X4B7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTN	I [auth A], J [auth B], K [auth C], L [auth D], N [auth E], O [auth F], P [auth G], Q [auth H]	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate C10 H18 N O3 S2 MXZPGYFBZHBAQM-UHFFFAOYSA-N
CL	M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.229 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.153	α = 90
b = 141.152	β = 90
c = 167.529	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Hagelueken, G., Ingledew, W.J., Huang, H., Petrovic-Stojanovska, B., Whitfield, C., ElMkami, H., Schiemann, O., Naismith, J.H.

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-05-12
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary