1CMA

MET REPRESSOR/DNA COMPLEX + S-ADENOSYL-METHIONINE

• PDB DOI: https://doi.org/10.2210/pdb1CMA/pdb
• NAKB: 1CMA

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1992-08-24 Released: 1993-10-31 
• Deposition Author(s): Somers, W.S., Phillips, S.E.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Observed: 0.220 

Literature

Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands.

Somers, W.S., Phillips, S.E.

(1992) Nature 359: 387-393

• PubMed: 1406951 
• DOI: https://doi.org/10.1038/359387a0
• Primary Citation of Related Structures:  
  1CMA


• PubMed Abstract: 
  

  The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognizes sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Leeds, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.63 kDa 
• Atom Count: 2,166 
• Modelled Residue Count: 227 
• Deposited Residue Count: 227 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (MET REPRESSOR)	C [auth A], D [auth B]	104	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A8U6 (Escherichia coli (strain K12)) Explore P0A8U6  Go to UniProtKB:  P0A8U6

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*AP*GP*AP*CP*GP*TP*CP*T)-3')	A [auth C]	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*AP*CP*GP*TP*CP*TP*A)-3')	B [auth D]	9	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	E [auth A], F [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Observed: 0.220 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.35	α = 90
b = 121.35	β = 90
c = 84.81	γ = 120

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Somers, W.S., Phillips, S.E.V.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations