4ABT | pdb_00004abt

Crystal structure of Type IIF restriction endonuclease NgoMIV with cognate uncleaved DNA

• PDB DOI: https://doi.org/10.2210/pdb4ABT/pdb
• NAKB: 4ABT

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


• Deposited: 2011-12-11 Released: 2011-12-28 
• Deposition Author(s): Manakova, E.N., Grazulis, S., Zaremba, M., Tamulaitiene, G., Golovenko, D., Siksnys, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved DNA

Manakova, E.N., Grazulis, S., Zaremba, M., Tamulaitiene, G., Golovenko, D., Siksnys, V.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.44 kDa 
• Atom Count: 5,188 
• Modeled Residue Count: 594 
• Deposited Residue Count: 594 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYPE-2 RESTRICTION ENZYME NGOMIV	A, B	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: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'	C [auth E], D [auth G]	11	Neisseria gonorrhoeae

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.899	α = 90
b = 90.081	β = 90
c = 92.711	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Manakova, E.N., Grazulis, S., Zaremba, M., Tamulaitiene, G., Golovenko, D., Siksnys, V.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Database references, Other
• Version 1.2: 2019-07-17
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2023-12-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description