5UA1 | pdb_00005ua1

Mycobacterium tuberculosis KstR in complex with a 18-bp DNA operator

• PDB DOI: https://doi.org/10.2210/pdb5UA1/pdb
• NAKB: 5UA1

• Classification: Transcription/DNA
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-18 Released: 2017-11-22 
• Deposition Author(s): Ho, N.A.T., Dawes, S.S., Baker, E.N., Lott, J.S., TB Structural Genomics Consortium (TBSGC)
• Funding Organization(s): Health Research Council (HRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of KstR in complex with cognate DNA operator

Ho, N.A.T., Dawes, S.S., Baker, E.N., Lott, J.S.

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.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.26 kDa 
• Atom Count: 4,047 
• Modeled Residue Count: 427 
• Deposited Residue Count: 478 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional repressor KstR	A [auth B], B [auth A]	203	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: kstR, Rv3574
UniProt
Find proteins for P96856 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P96856  Go to UniProtKB:  P96856

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*AP*T)-3')	C, E	18	Mycobacterium tuberculosis H37Rv

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*GP*T)-3')	D, F	18	Mycobacterium tuberculosis H37Rv

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	H [auth B], J [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	G [auth B], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.423	α = 90
b = 79.28	β = 90
c = 116.162	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Ho, N.A.T., Dawes, S.S., Baker, E.N., Lott, J.S., TB Structural Genomics Consortium (TBSGC)

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Funding Organization	Location	Grant Number
Health Research Council (HRC)	New Zealand	12/1111

Revision History  

• Version 1.0: 2017-11-22
  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