4E1J | pdb_00004e1j

Crystal structure of glycerol kinase in complex with glycerol from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb4E1J/pdb

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


• Deposited: 2012-03-06 Released: 2012-03-21 
• Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Siedel, 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: 2.33 Å
• R-Value Free: 
  0.290 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal structure of glycerol kinase in complex with glycerol from Sinorhizobium meliloti 1021

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 231.12 kDa 
• Atom Count: 14,333 
• Modeled Residue Count: 1,922 
• Deposited Residue Count: 2,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol kinase	A, B, C, D	520	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: glpK, RB1135, SMb21009 EC: 2.7.1.30
UniProt
Find proteins for O86033 (Rhizobium meliloti (strain 1021)) Explore O86033  Go to UniProtKB:  O86033

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], G [auth B], I [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A], J [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.290 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.22	α = 90
b = 101.975	β = 90.03
c = 107.548	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Siedel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary