1RKT

Crystal structure of yfiR, a putative transcriptional regulator from Bacillus subtilis

• PDB DOI:  https://doi.org/10.2210/pdb1RKT/pdb

• Classification: TRANSCRIPTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-11-23 Released: 2004-04-13 
• Deposition Author(s): Anderson, W.F., Rajan, S.S., Yang, X., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.254 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Crystal structure of YfiR, an unusual TetR/CamR-type putative transcriptional regulator from Bacillus subtilis.

Rajan, S.S., Yang, X., Shuvalova, L., Collart, F., Anderson, W.F.

(2006) Proteins 65: 255-257

• PubMed: 16862575 
• DOI: https://doi.org/10.1002/prot.21073
• Primary Citation of Related Structures:  
  1RKT

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 47.81 kDa 
• Atom Count: 3,548 
• Modelled Residue Count: 404 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein yfiR	A, B	205	Bacillus subtilis	Mutation(s): 4  Gene Names: yfiR
UniProt
Find proteins for O31560 (Bacillus subtilis (strain 168)) Explore O31560  Go to UniProtKB:  O31560

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], Q [auth A], R [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.254 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.983	α = 71.96
b = 48.765	β = 70.65
c = 57.233	γ = 80.2

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-13 
Deposition Author(s): Anderson, W.F., Rajan, S.S., Yang, X., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-04-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance