3F8M | pdb_00003f8m

Crystal Structure of PhnF from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb3F8M/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., Lott, S.J., Baker, E.N., Money, V.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.248 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

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

Busby, J.N., Gebhard, S., Cook, G.M., Lott, S.J., Baker, E.N., 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)

Macromolecule Content 

• Total Structure Weight: 54.62 kDa 
• Atom Count: 3,991 
• Modeled Residue Count: 455 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GntR-family protein transcriptional regulator	A, B	248	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_0650
UniProt
Find proteins for A0QQ72 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QQ72  Go to UniProtKB:  A0QQ72

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.248 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.501	α = 90
b = 76.954	β = 113.48
c = 66.897	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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