3KKE | pdb_00003kke

Crystal structure of a LacI family transcriptional regulator from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb3KKE/pdb

• Classification: transcription regulator
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-11-05 Released: 2009-12-08 
• Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Do, J., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.247 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal structure of a LacI family transcriptional regulator from Mycobacterium smegmatis

Bonanno, J.B., Rutter, M., Bain, K.T., Do, J., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 128.38 kDa 
• Atom Count: 8,251 
• Modeled Residue Count: 1,131 
• Deposited Residue Count: 1,212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LacI family Transcriptional regulator	A, B, C, D	303	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_0491
UniProt
Find proteins for A0QPR6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QPR6  Go to UniProtKB:  A0QPR6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A], F [auth A], G [auth B], H [auth C], I [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.247 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.599	α = 90
b = 65.468	β = 90.72
c = 116.034	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Do, J., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references