6OHH | pdb_00006ohh

Structure of EF1p2_mFAP2b bound to DFHBI

• PDB DOI: https://doi.org/10.2210/pdb6OHH/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-05 Released: 2020-04-08 
• Deposition Author(s): Doyle, L.A., Stoddard, B.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Incorporation of sensing modalities into de novo designed fluorescence-activating proteins

Klima, J.C., Doyle, L.A., Lee, J.D., Rappleye, M., Gagnon, L.A., Lee, M.Y., Barros, E.P., Vorobieva, A.A., Dou, J., Bremner, S., Jacob, S., Quon, J.S., Chow, C.M., Carter, L., Mack, D.L., Amaro, R.E., Vaughan, J.C., Berndt, A., Stoddard, B.L., Baker, D.

(2021) Nat Commun 12: 856

• DOI: https://doi.org/10.1038/s41467-020-18911-w

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.46 kDa 
• Atom Count: 2,160 
• Modelled Residue Count: 254 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EF1p2_mFAP2b	A, B	129	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
38E	D [auth A], F [auth B]	(5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one C12 H10 F2 N2 O2 ZDDIJYXDUBFLID-YHYXMXQVSA-N
CA	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.35	α = 90
b = 35.564	β = 90.68
c = 86.596	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Doyle, L.A., Stoddard, B.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM115545

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2021-02-17
  Changes: Database references, Derived calculations
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Refinement description