3MKL | pdb_00003mkl

Crystal structure of DNA-binding transcriptional dual regulator from Escherichia coli K-12

• PDB DOI: https://doi.org/10.2210/pdb3MKL/pdb

• Classification: Transcription regulator
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-15 Released: 2010-04-28 
• Deposition Author(s): Chang, C., Mack, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.247 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal structure of DNA-binding transcriptional dual regulator from Escherichia coli K-12

Chang, C., Mack, J., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 28.12 kDa 
• Atom Count: 1,976 
• Modeled Residue Count: 215 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator gadX	A, B	120	Escherichia coli K-12	Mutation(s): 0  Gene Names: gadX, yhiX, b3516, JW3484
UniProt
Find proteins for P37639 (Escherichia coli (strain K12)) Explore P37639  Go to UniProtKB:  P37639

Small Molecules

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: 2.15 Å
• R-Value Free:  0.247 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.972	α = 90
b = 81.856	β = 90
c = 165.065	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-28 
Deposition Author(s): Chang, C., Mack, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary