6NFP | pdb_00006nfp

1.7 Angstrom Resolution Crystal Structure of Arginase from Bacillus subtilis subsp. subtilis str. 168

• PDB DOI: https://doi.org/10.2210/pdb6NFP/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-12-20 Released: 2019-01-02 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Evdokimova, E., Grimshaw, S., Kwon, K., Savchenko, A., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.

Inniss, N.L., Minasov, G., Chang, C., Tan, K., Kim, Y., Maltseva, N., Stogios, P., Filippova, E., Michalska, K., Osipiuk, J., Jaroszewki, L., Godzik, A., Savchenko, A., Joachimiak, A., Anderson, W.F., Satchell, K.J.F.

(2025) Microbiol Resour Announc 14: e0020025-e0020025

• PubMed: 40391899 
• DOI: https://doi.org/10.1128/mra.00200-25
• Primary Citation of Related Structures:  
  5TR3, 5TV2, 5TY0, 5U1O, 5U2G, 5U47, 5UE1, 5UME, 5US8, 5USW, 5USX, 5UTX, 5UU6, 5UWY, 5UX9, 5V36, 5VDN, 5VFB, 5VH6, 5WI5, 5WP0, 6AON, 6AOO, 6AWA, 6AZI, 6B4O, 6B5F, 6B8D, 6BAL, 6BK7, 6BLB, 6BQ9, 6BZ0, 6C8Q, 6CMZ, 6CN1, 6CZP, 6E5Y, 6MUQ, 6N0I, 6N7F, 6NFP, 6NKJ, 6PO4, 6PU9, 6PUA, 6PXA, 6W2Z, 9BZN, 9BZQ


• PubMed Abstract: 
  

  Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

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Organizational Affiliation: 
• Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.
Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois, USA.
Biozone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Biosciences Division, University of California, Riverside, School of Medicine, Riverside, California, USA.
Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 200.28 kDa 
• Atom Count: 15,539 
• Modeled Residue Count: 1,737 
• Deposited Residue Count: 1,794 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginase	A, B, C, D, E, F	299	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: rocF, BSU40320, argI EC: 3.5.3.1
UniProt
Find proteins for P39138 (Bacillus subtilis (strain 168)) Explore P39138  Go to UniProtKB:  P39138

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	PA [auth B], QA [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	HB [auth C], IB [auth C], IC [auth E], JB [auth C], JC [auth E], KC [auth E], LA [auth B], MA [auth B], NA [auth B], OA [auth B], TB [auth D], UB [auth D], UC [auth F], VB [auth D], VC [auth F], WB [auth D], X [auth A], Y [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOA	FB [auth C], GB [auth C], SB [auth D], TC [auth F]	GLYCOLIC ACID C2 H4 O3 AEMRFAOFKBGASW-UHFFFAOYSA-N
EDO	CB [auth C], DB [auth C], EB [auth C], HC [auth E], JA [auth B], KA [auth B], RB [auth D], RC [auth F], S [auth A], SC [auth F], T [auth A], U [auth A], V [auth A], W [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
URE	AB [auth C], BB [auth C], FC [auth E], GA [auth B], GC [auth E], HA [auth B], IA [auth B], P [auth A], PC [auth F], Q [auth A], QC [auth F], R [auth A], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N
FMT	BC [auth E], CC [auth E], DA [auth B], DC [auth E], EA [auth B], EC [auth E], FA [auth B], N [auth A], NB [auth D], NC [auth F], O [auth A], OB [auth D], OC [auth F], PB [auth D], QB [auth D]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth A], KB [auth D], RA [auth C], SA [auth C], TA [auth C], XB [auth E], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	AC [auth E], BA [auth B], CA [auth B], L [auth A], LB [auth D], LC [auth F], M [auth A], MB [auth D], MC [auth F], UA [auth C], VA [auth C], ZB [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	AA [auth B], K [auth A], YB [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36nfp

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.414	α = 90
b = 143.989	β = 109.35
c = 85.515	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-02 
Deposition Author(s): Minasov, G., Wawrzak, Z., Evdokimova, E., Grimshaw, S., Kwon, K., Savchenko, A., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2019-01-02
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2026-02-11
  Changes: Database references, Structure summary