3HTZ | pdb_00003htz

Crystal Structure of the catalytic fragment of alanyl-tRNA synthetase in complex with L-serine: Re-refined

• PDB DOI: https://doi.org/10.2210/pdb3HTZ/pdb

• Classification: LIGASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-12 Released: 2009-06-30 
• Deposition Author(s): Guo, M., Swairjo, M.A., Schimmel, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.315 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1YGB

Literature

Serine Paradox

Guo, M., Schimmel, P.

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 (software)

Macromolecule Content 

• Total Structure Weight: 53.64 kDa 
• Atom Count: 3,690 
• Modeled Residue Count: 447 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanyl-tRNA synthetase	A	464	Aquifex aeolicus	Mutation(s): 0  Gene Names: alaS, aq_1293 EC: 6.1.1.7
UniProt
Find proteins for O67323 (Aquifex aeolicus (strain VF5)) Explore O67323  Go to UniProtKB:  O67323

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.315 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.091	α = 90
b = 74.091	β = 90
c = 173.595	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Guo, M., Swairjo, M.A., Schimmel, P.

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description