8D5V | pdb_00008d5v

WhiB6 bound to the SigmaAr4-RNAP Beta flap tip chimera

• PDB DOI: https://doi.org/10.2210/pdb8D5V/pdb

• Classification: TRANSCRIPTION/Transferase
• Organism(s): Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-06 Released: 2023-06-14 
• Deposition Author(s): Wan, T., Zhang, L.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.231 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of WhiB6 and SigA4-betaTip complex

Wan, T., Zhang, L.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.62 kDa 
• Atom Count: 2,951 
• Modeled Residue Count: 357 
• Deposited Residue Count: 456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulator WhiB6	A, C	116	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: whiB6, Rv3862c
UniProt
Find proteins for P9WF37 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WF37  Go to UniProtKB:  P9WF37

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta	B, D	112	Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis This entity is chimeric	Mutation(s): 0  Gene Names: sigA, mysA, rpoD, rpoV, Rv2703, MTCY05A6.24, rpoB, Rv0667, MTCI376.08c EC: 2.7.7.6
UniProt
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGI1  Go to UniProtKB:  P9WGI1
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY9  Go to UniProtKB:  P9WGY9
UniProt Groups	P9WGY9P9WGI1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4 (Subject of Investigation/LOI)	E [auth A], F [auth C]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.231 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.983	α = 90
b = 66.54	β = 90
c = 158.805	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Wan, T., Zhang, L.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM138157-01
National Science Foundation (NSF, United States)	United States	CLP 1846908

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2025-06-04
  Changes: Refinement description, Structure summary