3A4K

Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb3A4K/pdb
• NAKB: 3A4K

• Classification: HYDROLASE/DNA
• Organism(s): Haemophilus influenzae Rd KW20
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-09 Released: 2009-10-20 
• Deposition Author(s): Watanabe, N., Sato, C., Takasaki, Y., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.226 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations

Watanabe, N., Takasaki, Y., Sato, C., Ando, S., Tanaka, I.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1326-1333

• PubMed: 19966419 
• DOI: https://doi.org/10.1107/S0907444909041134
• Primary Citation of Related Structures:  
  2E52, 3A4K


• PubMed Abstract: 
  

  The three-dimensional crystal structures of HindIII bound to its cognate DNA with and without divalent cations were solved at 2.17 and 2.00 A resolution, respectively. HindIII forms a dimer. The structures showed that HindIII belongs to the EcoRI-like (alpha-class) subfamily of type II restriction endonucleases. The cognate DNA-complex structures revealed the specific DNA-recognition mechanism of HindIII by which it recognizes the palindromic sequence A/AGCTT. In the Mg(2+) ion-soaked structure the DNA was cleaved and two ions were bound at each active site, corresponding to the two-metal-ion mechanism.

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Organizational Affiliation: 

Department of Biotechnology and Biomaterial Chemistry, Graduate School of Engineering, Nagoya University, Japan. [e-mail]

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 163.08 kDa 
• Atom Count: 11,846 
• Modelled Residue Count: 1,261 
• Deposited Residue Count: 1,276 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type-2 restriction enzyme HindIII	A, B [auth C], C [auth B], D	301	Haemophilus influenzae Rd KW20	Mutation(s): 0  Gene Names: hindIIIR EC: 3.1.21.4
UniProt
Find proteins for P43870 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43870  Go to UniProtKB:  P43870

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*A)-3')	E, G, I, K	4	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')	F, H, J, L	8	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')	M, N	12	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	AA [auth D], Q [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	BA [auth D], T [auth C], W [auth B], X [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	P [auth A], S [auth C], V [auth B], Z [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	O [auth A], R [auth C], U [auth B], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.226 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.46	α = 90
b = 132.211	β = 111.03
c = 94.07	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Watanabe, N., Sato, C., Takasaki, Y., Tanaka, I.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2014-03-05
  Changes: Database references
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description