3F8L

Crystal Structure of the Effector Domain of PhnF from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb3F8L/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-12 Released: 2009-11-17 
• Deposition Author(s): Busby, J.N., Gebhard, S., Cook, G.M., Baker, E.N., Lott, S.J., Money, V.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.182 

Literature

Crystal structure of PhnF, a GntR-family transcription regulator in Mycobacterium smegmatis

Busby, J.N., Gebhard, S., Cook, G.M., Baker, E.N., Lott, S.J., Money, V.A.

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 2  

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

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

Macromolecule Content

• Total Structure Weight: 89.76 kDa 
• Atom Count: 5,720 
• Modelled Residue Count: 653 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional repressor phnF	A, B, C, D	201	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_0650, phnF
UniProt
Find proteins for A0QQ72 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QQ72  Go to UniProtKB:  A0QQ72

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.182 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.558	α = 90
b = 78.172	β = 125.42
c = 120.514	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Busby, J.N., Gebhard, S., Cook, G.M., Baker, E.N., Lott, S.J., Money, V.A.

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description