3ICA | pdb_00003ica

The crystal structure of the beta subunit of a phenylalanyl-tRNA synthetase from Porphyromonas gingivalis W83

• PDB DOI: https://doi.org/10.2210/pdb3ICA/pdb

• Classification: LIGASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-17 Released: 2009-07-28 
• Deposition Author(s): Fan, Y., Sather, A., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.255 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

The crystal structure of the beta subunit of a phenylalanyl-tRNA synthetase from Porphyromonas gingivalis W83

Fan, Y., Sather, A., Keigher, L., Joachimiak, A.

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: 50.24 kDa 
• Atom Count: 3,604 
• Modeled Residue Count: 412 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanyl-tRNA synthetase beta chain	A, B	213	Porphyromonas gingivalis	Mutation(s): 0  Gene Names: PG_0099, pheT, Porphyromonas gingivalis EC: 6.1.1.20
UniProt
Find proteins for Q7MXR4 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MXR4  Go to UniProtKB:  Q7MXR4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAM	J [auth B]	TRIS(HYDROXYETHYL)AMINOMETHANE C7 H17 N O3 GKODZWOPPOTFGA-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-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: 2.44 Å
• R-Value Free:  0.255 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.725	α = 90
b = 59.725	β = 90
c = 256.266	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Fan, Y., Sather, A., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary