5FAR

Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complex with 9-METHYLGUANINE

• PDB DOI: https://doi.org/10.2210/pdb5FAR/pdb

• Classification: LYASE
• Organism(s): Bacillus cereus BAG3X2-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-11 Released: 2016-01-13 
• Deposition Author(s): Chang, C., Maltseva, N., Kim, Y., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complex with 9-METHYLGUANINE

Chang, C., Maltseva, N., Kim, Y., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 116.21 kDa 
• Atom Count: 8,178 
• Modelled Residue Count: 956 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydroneopterin aldolase	A, B, C, D, E, F, G, H	123	Bacillus cereus BAG3X2-1	Mutation(s): 0  Gene Names: IE3_00005 EC: 4.1.2.25

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9MG	I [auth A], J [auth B], K [auth C], L [auth C], M [auth E], N [auth F], O [auth G], P [auth H]	9-METHYLGUANINE C6 H7 N5 O UUWJNBOCAPUTBK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m35far

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.795	α = 90
b = 138.209	β = 89.97
c = 63.933	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing
BUCCANEER	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Chang, C., Maltseva, N., Kim, Y., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary