5W7H | pdb_00005w7h

Supercharged arPTE variant R5

• PDB DOI: https://doi.org/10.2210/pdb5W7H/pdb

• Classification: HYDROLASE
• Organism(s): Agrobacterium tumefaciens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-19 Released: 2019-01-23 
• Deposition Author(s): Campbell, E., Grant, J., Wang, Y., Sandhu, M., Williams, R.J., Nisbet, D.R., Perriman, A., Lupton, D., Jackson, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Hydrogel-Immobilized Supercharged Proteins

Campbell, E., Grant, J., Wang, Y., Sandhu, M., Nisbet, D., Perriman, A., Lupton, D., Jackson, C.J.

(2018) Adv Biosyst 

• DOI: https://doi.org/10.1002/adbi.201700240

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)

Macromolecule Content 

• Total Structure Weight: 74.61 kDa 
• Atom Count: 5,128 
• Modeled Residue Count: 658 
• Deposited Residue Count: 682 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotriesterase	A, B	341	Agrobacterium tumefaciens	Mutation(s): 0  Gene Names: opdA
UniProt
Find proteins for Q93LD7 (Agrobacterium tumefaciens) Explore Q93LD7  Go to UniProtKB:  Q93LD7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.391	α = 90
b = 110.076	β = 90
c = 112.277	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Campbell, E., Grant, J., Wang, Y., Sandhu, M., Williams, R.J., Nisbet, D.R., Perriman, A., Lupton, D., Jackson, C.J.

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection