4DIM

Crystal structure of phosphoribosylglycinamide synthetase from Anaerococcus prevotii

• PDB DOI: https://doi.org/10.2210/pdb4DIM/pdb

• Classification: LIGASE
• Organism(s): Anaerococcus prevotii DSM 20548
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-31 Released: 2012-02-29 
• Deposition Author(s): Michalska, K., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.228 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Crystal structure of phosphoribosylglycinamide synthetase from Anaerococcus prevotii

Michalska, K., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.8 kDa 
• Atom Count: 3,093 
• Modelled Residue Count: 393 
• Deposited Residue Count: 403 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylglycinamide synthetase	A	403	Anaerococcus prevotii DSM 20548	Mutation(s): 0  Gene Names: Apre_1268
UniProt
Find proteins for C7RDM8 (Anaerococcus prevotii (strain ATCC 9321 / DSM 20548 / JCM 6508 / NCTC 11806 / PC1)) Explore C7RDM8  Go to UniProtKB:  C7RDM8

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.228 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M34DIM

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.27	α = 90
b = 84.467	β = 100.54
c = 49.642	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
Auto-Rickshaw	phasing
SHELX	model building
ABS	model building
HELICAP	model building
BUCCANEER	model building
Coot	model building
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Michalska, K., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary