3GO6

Crystal Structure of M. tuberculosis ribokinase (Rv2436) in complex with ribose and AMP-PNP

• PDB DOI: https://doi.org/10.2210/pdb3GO6/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-18 Released: 2010-03-31 
• Deposition Author(s): Masters, E.I., Sun, Y., Wang, Y., Parker, W.B., Li, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.203 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

Crystal structure and biochemical characterization of M.tuberculosis ribokinase (Rv2436)

Masters, E.I., Sun, Y., Wang, Y., Parker, W.B., Li, R.

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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.89 kDa 
• Atom Count: 4,556 
• Modelled Residue Count: 574 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOKINASE RBSK	A, B	310	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: rbsK, Rv2436 EC: 2.7.1.15
UniProt
Find proteins for P71913 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P71913  Go to UniProtKB:  P71913

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
RIB	C [auth A]	alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.203 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.424	α = 90
b = 117.9	β = 113.93
c = 91.571	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Masters, E.I., Sun, Y., Wang, Y., Parker, W.B., Li, R.

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-02-21
  Changes: Data collection, Database references, Structure summary