5ARD | pdb_00005ard

Cooperative bio-metallic selectivity in a tailored protease enables creation of a C-C cross-coupling Heckase

• PDB DOI: https://doi.org/10.2210/pdb5ARD/pdb

• Classification: HYDROLASE
• Organism(s): Lederbergia lenta
• Expression System: Bacillus subtilis
• Mutation(s): Yes 


• Deposited: 2015-09-24 Released: 2016-09-14 
• Deposition Author(s): Sharma, M., Diaz-Rodriguez, A., Offen, W.A., Palm-Espling, M.E., Pordea, A., Wormald, M.R., Mcdonough, M., Davies, G.J., Davis, B.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.154 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Cooperative Bio-Metallic Selectivity in a Tailored Protease Enables Creation of a C-C Cross-Coupling Heckase

Sharma, M., Diaz-Rodriguez, A., Offen, W.A., Palm-Espling, M.E., Pordea, A., Wormald, M.R., Mcdonough, M., Davies, G.J., Davis, B.G.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 27.27 kDa 
• Atom Count: 2,211 
• Modeled Residue Count: 269 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUBTILISIN SAVINASE	A	269	Lederbergia lenta	Mutation(s): 1  EC: 3.4.21.62
UniProt
Find proteins for P29600 (Lederbergia lenta) Explore P29600  Go to UniProtKB:  P29600

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EI3	E [auth A]	5-methyl-2-(5-methylpyridin-2-yl)pyridine C12 H12 N2 PTRATZCAGVBFIQ-UHFFFAOYSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	F [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.154 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.059	α = 90
b = 61.28	β = 90
c = 74.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Sharma, M., Diaz-Rodriguez, A., Offen, W.A., Palm-Espling, M.E., Pordea, A., Wormald, M.R., Mcdonough, M., Davies, G.J., Davis, B.G.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary