5F3M | pdb_00005f3m

Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complexed with L-neopterin at 1.5 Angstroms resolution .

• PDB DOI: https://doi.org/10.2210/pdb5F3M/pdb

• Classification: ISOMERASE
• Organism(s): Bacillus anthracis str. 'Ames Ancestor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-03 Released: 2015-12-23 
• Deposition Author(s): 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: 1.50 Å
• R-Value Free: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complexed with L-neopterin at 1.5 Angstroms resolution .

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 29.74 kDa 
• Atom Count: 2,440 
• Modeled Residue Count: 240 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydroneopterin aldolase	A, B	123	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0  Gene Names: folB EC: 4.1.2.25
UniProt
Find proteins for A0A6L7HSV1 (Bacillus anthracis) Explore A0A6L7HSV1  Go to UniProtKB:  A0A6L7HSV1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NEU	C [auth A], H [auth B]	L-NEOPTERIN C9 H11 N5 O4 BMQYVXCPAOLZOK-XINAWCOVSA-N
EDO	E [auth A], F [auth A], G [auth A], J [auth B], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	D [auth A], I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
FMT	L [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35f3m

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.974	α = 90
b = 87.974	β = 90
c = 104.549	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Maltseva, N., Kim, Y., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-12-23
  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: 2024-10-09
  Changes: Structure summary
• Version 1.4: 2025-10-22
  Changes: Database references, Structure summary