3R9L

Crystal structure of nucleoside diphosphate kinase from Giardia lamblia featuring a disordered dinucleotide binding site

• PDB DOI: https://doi.org/10.2210/pdb3R9L/pdb

• Classification: TRANSFERASE
• Organism(s): Giardia lamblia ATCC 50803
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-25 Released: 2011-04-20 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.266 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 

Starting Model: experimental

Literature

Crystal structure of nucleoside diphosphate kinase from Giardia lamblia featuring a disordered dinucleotide binding site

Edwards, T.E., Gardberg, A.S., Sankaran, B., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 17.15 kDa 
• Atom Count: 827 
• Modelled Residue Count: 112 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A	155	Giardia lamblia ATCC 50803	Mutation(s): 0  Gene Names: GL50803_11301 EC: 2.7.4.6
UniProt
Find proteins for A8BMG9 (Giardia intestinalis (strain ATCC 50803 / WB clone C6)) Explore A8BMG9  Go to UniProtKB:  A8BMG9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.266 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 
• Space Group: P 6₃ 2 2
• Diffraction Data: https://doi.org/10.18430/M33R9L

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.96	α = 90
b = 116.96	β = 90
c = 62.69	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description