2XD4 | pdb_00002xd4

Nucleotide-bound Structures of Bacillus subtilis Glycinamide Ribonucleotide Synthetase

• PDB DOI: https://doi.org/10.2210/pdb2XD4/pdb

• Classification: LIGASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-04-29 Released: 2011-03-23 
• Deposition Author(s): Bertrand, J.A., Chen, S., Zalkin, H., Smith, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.270 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase

Bertrand, J.A., Chen, S., Zalkin, H., Smith, J.L.

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: 45.83 kDa 
• Atom Count: 3,265 
• Modeled Residue Count: 422 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYLAMINE--GLYCINE LIGASE	A	422	Bacillus subtilis	Mutation(s): 0  EC: 6.3.4.13
UniProt
Find proteins for P12039 (Bacillus subtilis (strain 168)) Explore P12039  Go to UniProtKB:  P12039

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.270 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.99	α = 90
b = 84.41	β = 90
c = 85.72	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-23 
Deposition Author(s): Bertrand, J.A., Chen, S., Zalkin, H., Smith, J.L.

Revision History  

• Version 1.0: 2011-03-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-05
  Changes: Data collection
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description