2YY5 | pdb_00002yy5

Crystal Structure of tryptophanyl-tRNA synthetase from Mycoplasma pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb2YY5/pdb

• Classification: LIGASE
• Organism(s): Mycoplasmoides pneumoniae M129
• Mutation(s): Yes 


• Deposited: 2007-04-27 Released: 2008-04-29 
• Deposition Author(s): Ishii, T., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of tryptophanyl-tRNA synthetase from Mycoplasma pneumoniae

Ishii, T., Bessho, Y., 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)

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: 160.14 kDa 
• Atom Count: 11,474 
• Modeled Residue Count: 1,362 
• Deposited Residue Count: 1,392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanyl-tRNA synthetase	A, B, C, D	348	Mycoplasmoides pneumoniae M129	Mutation(s): 1  EC: 6.1.1.2
UniProt
Find proteins for P75510 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75510  Go to UniProtKB:  P75510

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WSA	G [auth A], J [auth B], M [auth C], P [auth D]	5'-O-[(L-TRYPTOPHYLAMINO)SULFONYL]ADENOSINE C21 H24 N8 O7 S RQAVKMXDGHWLGD-BFNSABJLSA-N
SO4	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], N [auth D], O [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.163	α = 90
b = 52.109	β = 96.05
c = 194.092	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Ishii, T., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-10-25
  Changes: Data collection, Refinement description