2D4W

Crystal structure of glycerol kinase from Cellulomonas sp. NT3060

• PDB DOI: https://doi.org/10.2210/pdb2D4W/pdb

• Classification: TRANSFERASE
• Organism(s): Cellulomonas sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-10-24 Released: 2006-11-14 
• Deposition Author(s): Imada, K., Tamura, T., Namba, K., Inagaki, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.240 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Structure of glycerol kinase from Cellulomonas sp. NT3060

Imada, K., Tamura, T., Inagaki, K.

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)

Macromolecule Content

• Total Structure Weight: 110.86 kDa 
• Atom Count: 8,139 
• Modelled Residue Count: 1,006 
• Deposited Residue Count: 1,008 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerol kinase	A, B	504	Cellulomonas sp.	Mutation(s): 0  EC: 2.7.1.30

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A], E [auth B], F [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.240 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.43	α = 90
b = 105.43	β = 90
c = 195.715	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-14 
Deposition Author(s): Imada, K., Tamura, T., Namba, K., Inagaki, K.

Revision History  

• Version 1.0: 2006-11-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations