1FIU | pdb_00001fiu

TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA

• PDB DOI: https://doi.org/10.2210/pdb1FIU/pdb
• NAKB: 1FIU

• Classification: hydrolase/DNA
• Organism(s): Neisseria gonorrhoeae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-08-07 Released: 2001-02-07 
• Deposition Author(s): Deibert, M., Grazulis, S., Sasnauskas, G., Siksnys, V., Huber, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.204 (Depositor) 
• R-Value Work: 
  0.173 (Depositor) 

Literature

Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA.

Deibert, M., Grazulis, S., Sasnauskas, G., Siksnys, V., Huber, R.

(2000) Nat Struct Biol 7: 792-799

• PubMed: 10966652 
• DOI: https://doi.org/10.1038/79032
• Primary Citation Related Structures: 
  1FIU


• PubMed Abstract: 
  

  The crystal structure of the NgoMIV restriction endonuclease in complex with cleaved DNA has been determined at 1.6 A resolution. The crystallographic asymmetric unit contains a protein tetramer and two DNA molecules cleaved at their recognition sites. This is the first structure of a tetrameric restriction enzyme-DNA complex. In the tetramer, two primary dimers are arranged back to back with two oligonucleotides bound in clefts on opposite sides of the tetramer. The DNA molecules retain a B-type conformation and have an enclosed angle between their helical axes of 60 degrees. Sequence-specific interactions occur in both the major and minor grooves. Two Mg2+ ions are located close to the cleaved phosphate at the active site of NgoMIV. Biochemical experiments show that interactions between the recognition sites within the tetramer greatly increase DNA cleavage efficiency.

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Organizational Affiliation: 
• Max-Planck-Institut für Biochemie, D-82152 Planegg-Martinsried, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 140.9 kDa 
• Atom Count: 11,147 
• Modeled Residue Count: 1,188 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TYPE II RESTRICTION ENZYME NGOMI	I [auth A], J [auth B], K [auth C], L [auth D]	286	Neisseria gonorrhoeae	Mutation(s): 0  EC: 3.1.21.4
UniProt
Find proteins for P31032 (Neisseria gonorrhoeae) Explore P31032  Go to UniProtKB:  P31032

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*CP*G)-3')	A [auth E], C [auth F], E [auth G], G [auth H]	4	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')	B [auth I], D [auth J], F [auth K], H [auth L]	7	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	R [auth A], T [auth B], V [auth C], X [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
MG	M [auth I], N [auth J], O [auth K], P [auth L], Q [auth A], S [auth B], U [auth C], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.204 (Depositor) 
• R-Value Work:  0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.4	α = 90
b = 91.13	β = 90
c = 149.52	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-07 
Deposition Author(s): Deibert, M., Grazulis, S., Sasnauskas, G., Siksnys, V., Huber, R.

Revision History  

• Version 1.0: 2001-02-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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