3LP8 | pdb_00003lp8

Crystal structure of phosphoribosylamine-glycine ligase from Ehrlichia chaffeensis

• PDB DOI: https://doi.org/10.2210/pdb3LP8/pdb

• Classification: LIGASE
• Organism(s): Ehrlichia chaffeensis str. Arkansas
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-04 Released: 2010-02-23 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of phosphoribosylamine-glycine ligase from Ehrlichia chaffeensis

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Sankaran, B., Davies, D., Staker, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.55 kDa 
• Atom Count: 3,420 
• Modeled Residue Count: 421 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylamine-glycine ligase	A	442	Ehrlichia chaffeensis str. Arkansas	Mutation(s): 0  Gene Names: purD, ECH_1006 EC: 6.3.4.13
UniProt
Find proteins for Q2GFJ0 (Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas)) Explore Q2GFJ0  Go to UniProtKB:  Q2GFJ0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
UNX	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LP8

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.85	α = 90
b = 74.16	β = 90
c = 107.29	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description