3OJ0 | pdb_00003oj0

Crystal structure of glutamyl-tRNA reductase from Thermoplasma volcanium (nucleotide binding domain)

• PDB DOI: https://doi.org/10.2210/pdb3OJ0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermoplasma volcanium GSS1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-08-20 Released: 2010-09-01 
• Deposition Author(s): Michalska, K., Marshall, N., Clancy, S., Puttagunta, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.183 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal structure of glutamyl-tRNA reductase from Thermoplasma volcanium (nucleotide binding domain)

Michalska, K., Marshall, N., Clancy, S., Puttagunta, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.18 kDa 
• Atom Count: 1,277 
• Modelled Residue Count: 138 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamyl-tRNA reductase	A	144	Thermoplasma volcanium GSS1	Mutation(s): 0  Gene Names: hemA, TV0590, TVG0579613 EC: 1.2.1.70
UniProt
Find proteins for Q97B68 (Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)) Explore Q97B68  Go to UniProtKB:  Q97B68

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.183 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.52	α = 90
b = 92.52	β = 90
c = 33.47	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Michalska, K., Marshall, N., Clancy, S., Puttagunta, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary