2NWH | pdb_00002nwh

Carbohydrate kinase from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb2NWH/pdb

• Classification: SIGNALING PROTEIN,TRANSFERASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-11-14 Released: 2006-12-12 
• Deposition Author(s): Osipiuk, J., Xu, X., Gu, J., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.233 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

X-ray crystal structure of carbohydrate kinase from Agrobacterium tumefaciens

Osipiuk, J., Xu, X., Gu, J., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 33.46 kDa 
• Atom Count: 2,617 
• Modeled Residue Count: 307 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
carbohydrate kinase	A	317	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu1875
UniProt
Find proteins for A9CII5 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CII5  Go to UniProtKB:  A9CII5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.233 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.93	α = 90
b = 75.93	β = 90
c = 103.608	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
SOLVE	phasing
RESOLVE	model building
HKL-2000	data scaling
REFMAC	refinement
HKL-2000	data reduction
HKL-3000	phasing
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Osipiuk, J., Xu, X., Gu, J., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations