6WUQ

Crystal structure of AjiA1 in apo form

• PDB DOI: https://doi.org/10.2210/pdb6WUQ/pdb

• Classification: LIGASE
• Organism(s): Streptomyces sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-05 Released: 2020-12-09 
• Deposition Author(s): Paiva, F.C.R., Chan, K., Leadlay, P., Dias, M.V.B.
• Funding Organization(s): Sao Paulo Research Foundation, Brazilian National Council for Scientific and Technological Development

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family

Paiva, F.C.R., Chan, K., Samborskyy, M., Silber, A.M., Leadlay, P., Dias, M.V.B.

(2020) Acta Crystallogr D Biol Crystallogr 76: 1201

• DOI: https://doi.org/10.1107/S2059798320013431

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: gel filtration

Macromolecule Content

• Total Structure Weight: 96.86 kDa 
• Atom Count: 6,869 
• Modelled Residue Count: 859 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AjiA1	A, B	436	Streptomyces sp.	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.777	α = 90
b = 128.777	β = 90
c = 101.449	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Paiva, F.C.R., Chan, K., Leadlay, P., Dias, M.V.B.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation	Brazil	2018/003511
Brazilian National Council for Scientific and Technological Development	Brazil	141090/2016-2

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description