5F9Y | pdb_00005f9y

Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Proline and AMP

• PDB DOI: https://doi.org/10.2210/pdb5F9Y/pdb

• Classification: LIGASE
• Organism(s): Cryptosporidium parvum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-10 Released: 2016-11-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.243 (Depositor) 
• R-Value Work: 
  0.214 (Depositor) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Proline and AMP

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Dranow, D.M., Fox III, D., Lorimer, D., Edwards, T.E.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 119.77 kDa 
• Atom Count: 7,461 
• Modeled Residue Count: 955 
• Deposited Residue Count: 1,022 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoacyl-tRNA synthetase	A, B	511	Cryptosporidium parvum	Mutation(s): 0  Gene Names: 1MB.635

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	D [auth A], G [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
PRO	C [auth A], F [auth B]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
PO4	I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	E [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.243 (Depositor) 
• R-Value Work:  0.214 (Depositor) 
• R-Value Observed: 0.216 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35F9Y

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.87	α = 90
b = 110.14	β = 90
c = 127.71	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description