8PKR | pdb_00008pkr

Crystal structure of PknD-345, a repeat fragment from the M. tuberculosis PknD beta-propeller

• PDB DOI: https://doi.org/10.2210/pdb8PKR/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2023-06-27 Released: 2024-07-10 
• Deposition Author(s): Wouters, S.M.L.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.137 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Literature

Computational design of the SAKe scaffold proteins

Wouters, S.M.L., Noguchi, H., Voet, A.R.D.

To be published.

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: 27.37 kDa 
• Atom Count: 2,214 
• Modeled Residue Count: 245 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
non-specific serine/threonine protein kinase	A, B	128	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: pknD_1, pknD_2, ERS007657_00042, ERS007663_00011, ERS007665_00696, ERS007720_00884, SAMEA2683035_02262 EC: 2.7.11.1
UniProt
Find proteins for P9WI79 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WI79  Go to UniProtKB:  P9WI79

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.137 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.701	α = 90
b = 83.241	β = 90
c = 83.453	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Wouters, S.M.L.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	1S89918N
Research Foundation - Flanders (FWO)	Belgium	G0F9316N
Research Foundation - Flanders (FWO)	Belgium	G051917N

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release