3T61 | pdb_00003t61

Crystal Structure of a gluconokinase from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb3T61/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): Kumaran, D., 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: 2.20 Å
• R-Value Free: 
  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Crystal Structure of a gluconokinase from Sinorhizobium meliloti 1021

Kumaran, D., 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: 45.5 kDa 
• Atom Count: 2,860 
• Modeled Residue Count: 351 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gluconokinase	A, B	202	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: gntK, RB0698, SM_b21119 EC: 2.7.1.12
UniProt
Find proteins for Q92VK3 (Rhizobium meliloti (strain 1021)) Explore Q92VK3  Go to UniProtKB:  Q92VK3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.202	α = 90
b = 68.202	β = 90
c = 118.621	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-17 
Deposition Author(s): Kumaran, D., 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: 2012-03-21
  Changes: Structure summary
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary