1BDI

PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1BDI/pdb
• NAKB: 1BDI

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


• Deposited: 1996-07-25 Released: 1997-04-21 
• Deposition Author(s): Glasfeld, A., Schumacher, M.A., Choi, K.Y., Zalkin, H., Brennan, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Observed: 0.157 

Literature

A Positively Charged Residue Bound in the Minor Groove Does not Alter the Bending of a DNA Duplex

Glasfeld, A., Schumacher, M.A., Choi, K.Y., Zalkin, H., Brennan, R.G.

(1996) J Am Chem Soc 118: 13073-13074

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: 43.43 kDa 
• Atom Count: 3,009 
• Modelled Residue Count: 355 
• Deposited Residue Count: 357 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PURINE REPRESSOR)	B [auth A]	340	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ACP7 (Escherichia coli (strain K12)) Explore P0ACP7  Go to UniProtKB:  P0ACP7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')	A [auth B]	17	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HPA	C [auth A]	HYPOXANTHINE C5 H4 N4 O FDGQSTZJBFJUBT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HPA	PDBBind:  1BDI	Kd: 2.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Observed: 0.157 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.16	α = 90
b = 94.99	β = 90
c = 81.57	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement
UCSD	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-04-21 
Deposition Author(s): Glasfeld, A., Schumacher, M.A., Choi, K.Y., Zalkin, H., Brennan, R.G.

Revision History  

• Version 1.0: 1997-04-21
  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: 2024-02-07
  Changes: Data collection, Database references, Derived calculations