Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 24.42 kDa 
• Atom Count: 1456 
• Modelled Residue Count: 179 
• Deposited Residue Count: 194 
• Unique protein chains: 1

6OWX

Spy H96L:Im7 L18pI-Phe complex; multiple anomalous datasets contained herein for element identification

• PDB DOI: 10.2210/pdb6OWX/pdb

• Classification: CHAPERONE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-05-12 Released: 2019-05-29 
• Deposition Author(s): Rocchio, S., Duman, R., El Omari, K., Mykhaylyk, V., Yan, Z., Wagner, A., Bardwell, J.C.A., Horowitz, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.277 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 

Literature

Identifying dynamic, partially occupied residues using anomalous scattering.

Rocchio, S., Duman, R., El Omari, K., Mykhaylyk, V., Orr, C., Yan, Z., Salmon, L., Wagner, A., Bardwell, J.C.A., Horowitz, S.

(2019) Acta Crystallogr D Struct Biol 75: 1084-1095

• PubMed: 31793902 
• DOI: 10.1107/S2059798319014475
• Primary Citation of Related Structures:  
  6OWX, 6OWY, 6OWZ


• PubMed Abstract: 
  

Although often presented as taking single `snapshots' of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes residual electron and anomalous density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data-collection and analysis strategy for partially occupied iodine anomalous signals. Using the long-wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as ∼12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that re-measured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic chaperone Spy	A, B	97	Escherichia coli	Mutation(s): 1
UniProt
Find proteins for P77754 (Escherichia coli (strain K12)) Explore P77754  Go to UniProtKB:  P77754

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD (Subject of Investigation/LOI)	W [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
IMD	N [auth A], O [auth A], P [auth A], Q [auth A], S [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], R [auth A], T [auth B], U [auth B], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.277 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 
• Space Group: P 4₁ 2 2
• Diffraction Data DOI: 10.18430/m36owx Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.8	α = 90
b = 42.8	β = 90
c = 253.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-05-12 
• Released Date: 2019-05-29 
Deposition Author(s): Rocchio, S., Duman, R., El Omari, K., Mykhaylyk, V., Yan, Z., Wagner, A., Bardwell, J.C.A., Horowitz, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R00 GM120388
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-06-05
  Changes: Data collection, Database references, Structure summary
• Version 2.0: 2019-10-09
  Type: Coordinate replacement
  Reason: Atoms with unrealistic or zero occupancies
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Other, Refinement description, Structure summary
• Version 2.1: 2019-11-20
  Changes: Author supporting evidence
• Version 2.2: 2019-12-11
  Changes: Database references