3NGF | pdb_00003ngf

Crystal structure of AP endonuclease, family 2 from Brucella melitensis

• PDB DOI: https://doi.org/10.2210/pdb3NGF/pdb

• Classification: ISOMERASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-11 Released: 2010-07-07 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.176 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AP endonuclease, family 2 from Brucella melitensis

Staker, B., Edwards, T., Bullen, J., Dieterich, M., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 61.6 kDa 
• Atom Count: 4,895 
• Modeled Residue Count: 518 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP endonuclease, family 2	A, B	269	Brucella abortus 2308	Mutation(s): 0  Gene Names: BAB2_0144 EC: 5.3.1.22
UniProt
Find proteins for Q2YLA2 (Brucella abortus (strain 2308)) Explore Q2YLA2  Go to UniProtKB:  Q2YLA2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	C [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.176 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.98	α = 90
b = 120.64	β = 117.14
c = 54.68	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description