4HRI | pdb_00004hri

Crystal structure of HetR in complex with a 21-bp palindromic DNA at the upstream of the hetP promoter from Anabaena

• PDB DOI: https://doi.org/10.2210/pdb4HRI/pdb
• NAKB: 4HRI

• Classification: TRANSCRIPTION/DNA
• Organism(s): Nostoc sp. PCC 7120 = FACHB-418
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-28 Released: 2013-04-17 
• Deposition Author(s): Hu, H.X., Jiang, Y.L., Zhao, M.X., Chen, Y., Zhang, C.C., Zhou, C.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.307 (Depositor), 0.316 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Structural and biochemical analyses of Anabaena HetR reveal insights into its binding to DNA targets and the inhibitory hexapeptide ERGSGR

Hu, H.X., Jiang, Y.L., Zhao, M.X., Zhu, P.F., Yang, X.Y., Wen, B., Zhang, Z., Wu, Q., Chen, Y., Zhang, C.C., Zhou, C.Z.

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)

Macromolecule Content 

• Total Structure Weight: 85.08 kDa 
• Atom Count: 5,417 
• Modeled Residue Count: 594 
• Deposited Residue Count: 656 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterocyst differentiation control protein	A [auth B], B [auth A]	307	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0  Gene Names: hetR EC: 3.4.21
UniProt
Find proteins for P27709 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore P27709  Go to UniProtKB:  P27709

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*GP*AP*GP*GP*GP*GP*TP*CP*TP*AP*AP*CP*CP*CP*CP*TP*CP*AP*T)-3')	C	21	Nostoc sp. PCC 7120 = FACHB-418

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*GP*AP*CP*CP*CP*CP*TP*CP*GP*C)-3')	D	21	Nostoc sp. PCC 7120 = FACHB-418

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth C], F [auth C], G [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.307 (Depositor), 0.316 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.883	α = 90
b = 89.883	β = 90
c = 242.288	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Hu, H.X., Jiang, Y.L., Zhao, M.X., Chen, Y., Zhang, C.C., Zhou, C.Z.

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description