7WH4

Crystal structure of the PadR-family transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv in complex with Manganese ion

• PDB DOI: https://doi.org/10.2210/pdb7WH4/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-12-29 Released: 2022-02-09 
• Deposition Author(s): Arora, A., Zohib, M., Biswal, B.K., Pal, R.K.
• Funding Organization(s): Department of Science & Technology (DST, India)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.272 
• R-Value Work: 0.221 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

Crystal structure of PadR-family transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv in complex with Manganese ion

Arora, A., Zohib, M., Biswal, B.K., Pal, R.K.

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: 25.39 kDa 
• Atom Count: 1,575 
• Modelled Residue Count: 202 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator Rv3488	A, B	113	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv3488
UniProt
Find proteins for I6X7F9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6X7F9  Go to UniProtKB:  I6X7F9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.272 
• R-Value Work: 0.221 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.491	α = 90
b = 47.899	β = 90
c = 129.878	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Arora, A., Zohib, M., Biswal, B.K., Pal, R.K.

---

Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	--

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 2.0: 2022-03-23
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-29
  Changes: Data collection, Refinement description