3CXM | pdb_00003cxm

Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil

• PDB DOI: https://doi.org/10.2210/pdb3CXM/pdb

• Classification: HYDROLASE
• Organism(s): Leishmania naiffi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-04-24 Released: 2008-05-06 
• Deposition Author(s): Larson, E.T., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Structures of Leishmania naiffi uracil-DNA glycosylase in complex with several ligands identified with fragment cocktail crystallography.

Larson, E.T., Merritt, E.A.

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)

Macromolecule Content 

• Total Structure Weight: 30.76 kDa 
• Atom Count: 2,288 
• Modeled Residue Count: 242 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A	268	Leishmania naiffi	Mutation(s): 0  Gene Names: similar to LbrM18_V2.0540 EC: 3.2.2 (PDB Primary Data), 3.2.2.27 (UniProt)
UniProt
Find proteins for D0VWU0 (Leishmania naiffi) Explore D0VWU0  Go to UniProtKB:  D0VWU0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URB	C [auth A]	5-bromopyrimidine-2,4(1H,3H)-dione C4 H3 Br N2 O2 LQLQRFGHAALLLE-UHFFFAOYSA-N
URA	D [auth A]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR	B [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.32	α = 90
b = 75.32	β = 90
c = 105.703	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Larson, E.T., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description