6WHJ | pdb_00006whj

Structure of Ribokinase from Giardia lamblia

• PDB DOI: https://doi.org/10.2210/pdb6WHJ/pdb

• Classification: TRANSFERASE
• Organism(s): Giardia lamblia ATCC 50803
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-04-08 Released: 2020-04-22 
• 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: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure of Ribokinase from Giardia lamblia

Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 150.38 kDa 
• Atom Count: 9,743 
• Modeled Residue Count: 1,304 
• Deposited Residue Count: 1,404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B, C, D	351	Giardia lamblia ATCC 50803	Mutation(s): 0  Gene Names: GL50803_15297 EC: 2.7.1.15
UniProt
Find proteins for A8B6Y7 (Giardia intestinalis (strain ATCC 50803 / WB clone C6)) Explore A8B6Y7  Go to UniProtKB:  A8B6Y7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth B], G [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.62	α = 90
b = 169.92	β = 98.36
c = 84.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MR-Rosetta	phasing
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 1.1: 2020-07-01
  Changes: Data collection
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description