2H98

Crystal structure of the effector binding domain of a CatM variant, CatM(V158M)

• PDB DOI: https://doi.org/10.2210/pdb2H98/pdb

• Classification: TRANSCRIPTION
• Organism(s): Acinetobacter baylyi ADP1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-06-09 Released: 2007-06-26 
• Deposition Author(s): Ezezika, O.C., Neidle, E.L., Momany, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.232 
• R-Value Work: 0.167 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Structural basis for the altered regulatory roles of three LysR-type transcritional variants of CatM and BenM: CatM(V158M), CatM(R156H) and BenM(R156H/T157S)

Ezezika, O.C., Neidle, E.L., Momany, 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.

Macromolecule Content

• Total Structure Weight: 70.93 kDa 
• Atom Count: 4,146 
• Modelled Residue Count: 432 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator catM	A, B	313	Acinetobacter baylyi ADP1	Mutation(s): 1  Gene Names: catM, catR
UniProt
Find proteins for P07774 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P07774  Go to UniProtKB:  P07774

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.232 
• R-Value Work: 0.167 
• R-Value Observed: 0.171 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.447	α = 69.55
b = 51.038	β = 89.51
c = 59.12	γ = 77.63

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Ezezika, O.C., Neidle, E.L., Momany, C.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2021-10-20
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description