2DQ3 | pdb_00002dq3

Crystal structure of aq_298

• PDB DOI: https://doi.org/10.2210/pdb2DQ3/pdb

• Classification: LIGASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-18 Released: 2007-06-05 
• Deposition Author(s): Itoh, Y., Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.297 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of aq_298

Itoh, Y., Sekine, S., Yokoyama, 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: 100.17 kDa 
• Atom Count: 7,107 
• Modeled Residue Count: 850 
• Deposited Residue Count: 850 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seryl-tRNA synthetase	A, B	425	Aquifex aeolicus VF5	Mutation(s): 3  Gene Names: serS EC: 6.1.1.11
UniProt
Find proteins for O66647 (Aquifex aeolicus (strain VF5)) Explore O66647  Go to UniProtKB:  O66647

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SSA	C [auth A], D [auth B]	5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE C13 H19 N7 O8 S HQXFJGONGJPTLZ-YTMOPEAISA-N

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: 3.00 Å
• R-Value Free:  0.297 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.057	α = 90
b = 119.057	β = 90
c = 80.66	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-05 
Deposition Author(s): Itoh, Y., Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-06-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary