3T69 | pdb_00003t69

Crystal structure of a putative 2-dehydro-3-deoxygalactonokinase protein from Sinorhizobium meliloti

• PDB DOI: https://doi.org/10.2210/pdb3T69/pdb

• Classification: TRANSFERASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-07-28 Released: 2011-08-17 
• Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.277 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Crystal structure of a putative 2-dehydro-3-deoxygalactonokinase protein from Sinorhizobium meliloti

Agarwal, R., Almo, S.C., Swaminathan, S.

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: 70.12 kDa 
• Atom Count: 4,491 
• Modeled Residue Count: 605 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 2-dehydro-3-deoxygalactonokinase	A, B	330	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: dgoK1, R00825, SMc00881 EC: 2.7.1.58
UniProt
Find proteins for Q92RN7 (Rhizobium meliloti (strain 1021)) Explore Q92RN7  Go to UniProtKB:  Q92RN7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.277 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.398	α = 90
b = 109.741	β = 90
c = 121.134	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
CCP4	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-17 
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations