6CYZ | pdb_00006cyz

Mycobacterial homoserine kinase ThrB in complex with AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb6CYZ/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacteroides abscessus ATCC 19977
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-04-07 Released: 2018-04-18 
• Deposition Author(s): Li, J., Korotkov, K.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Mycobacterial homoserine kinase ThrB

Li, J., Korotkov, K.V.

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: 63.18 kDa 
• Atom Count: 4,487 
• Modeled Residue Count: 590 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine kinase	A, B	308	Mycobacteroides abscessus ATCC 19977	Mutation(s): 0  Gene Names: thrB, MAB_1437 EC: 2.7.1.39
UniProt
Find proteins for B1MLU6 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948)) Explore B1MLU6  Go to UniProtKB:  B1MLU6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	C [auth A], E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.35	α = 90
b = 62.7	β = 104.4
c = 84.63	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Li, J., Korotkov, K.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110787

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description