3ORK | pdb_00003ork

Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 2)

• PDB DOI: https://doi.org/10.2210/pdb3ORK/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Ra
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-09-07 Released: 2010-12-15 
• Deposition Author(s): Echols, N., Lombana, T.N., Thomsen, N.D., Ng, H.-L., Alber, T., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.180 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr kinase, PknB

Lombana, T.N., Echols, N., Good, M.C., Thomsen, N.D., Ng, H.-L., Greenstein, A.E., Falick, A.M., King, D.S., Alber, T.

(2010) Structure 18: 1667-1677

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: 34.32 kDa 
• Atom Count: 2,593 
• Modeled Residue Count: 274 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine protein kinase	A	311	Mycobacterium tuberculosis H37Ra	Mutation(s): 1  Gene Names: MRA_0016, pknB, PknB (Rv0014c) EC: 2.7.11.1
UniProt
Find proteins for P9WI81 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WI81  Go to UniProtKB:  P9WI81

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	B [auth A]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.180 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.341	α = 90
b = 51.603	β = 90
c = 155.126	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Echols, N., Lombana, T.N., Thomsen, N.D., Ng, H.-L., Alber, T., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description