Macromolecule Content

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

6NFP

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

PDB DOI: 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.166
R-Value Work: 0.139
R-Value Observed: 0.141

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

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)

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginase	A, B, C, D, E, F 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39138
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain PA [auth B] SDF format, chain QA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B]	PA [auth B], QA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain IC [auth E] SDF format, chain JB [auth C] SDF format, chain JC [auth E] SDF format, chain KC [auth E] SDF format, chain OA [auth B] SDF format, chain TB [auth D] SDF format, chain UB [auth D] SDF format, chain UC [auth F] SDF format, chain VB [auth D] SDF format, chain VC [auth F] SDF format, chain WB [auth D] SDF format, chain X [auth A] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain Y [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain IC [auth E] MOL2 format, chain JB [auth C] MOL2 format, chain JC [auth E] MOL2 format, chain KC [auth E] MOL2 format, chain OA [auth B] MOL2 format, chain TB [auth D] MOL2 format, chain UB [auth D] MOL2 format, chain UC [auth F] MOL2 format, chain VB [auth D] MOL2 format, chain VC [auth F] MOL2 format, chain WB [auth D] MOL2 format, chain X [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain Y [auth A]	HB [auth C], IB [auth C], IC [auth E], JB [auth C], JC [auth E], 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		Ligand Interaction
GOA Query on GOA Download Ideal Coordinates CCD File SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain SB [auth D] SDF format, chain TC [auth F] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain SB [auth D] MOL2 format, chain TC [auth F]	FB [auth C], GB [auth C], SB [auth D], TC [auth F]	GLYCOLIC ACID C₂ H₄ O₃ AEMRFAOFKBGASW-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain HC [auth E] SDF format, chain KA [auth B] SDF format, chain RB [auth D] SDF format, chain RC [auth F] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain JA [auth B] SDF format, chain S [auth A] SDF format, chain SC [auth F] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain HC [auth E] MOL2 format, chain KA [auth B] MOL2 format, chain RB [auth D] MOL2 format, chain RC [auth F] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SC [auth F] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A]	CB [auth C], DB [auth C], EB [auth C], HC [auth E], JA [auth B], 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		Ligand Interaction
URE Query on URE Download Ideal Coordinates CCD File SDF format, chain FC [auth E] SDF format, chain GA [auth B] SDF format, chain GC [auth E] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain Q [auth A] SDF format, chain QC [auth F] SDF format, chain XA [auth C] SDF format, chain ZA [auth C] SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain P [auth A] SDF format, chain PC [auth F] SDF format, chain R [auth A] SDF format, chain WA [auth C] SDF format, chain YA [auth C] MOL2 format, chain FC [auth E] MOL2 format, chain GA [auth B] MOL2 format, chain GC [auth E] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QC [auth F] MOL2 format, chain XA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PC [auth F] MOL2 format, chain R [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain YA [auth C]	AB [auth C], BB [auth C], FC [auth E], GA [auth B], GC [auth E], 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		Ligand Interaction
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain DC [auth E] SDF format, chain EA [auth B] SDF format, chain EC [auth E] SDF format, chain FA [auth B] SDF format, chain N [auth A] SDF format, chain NB [auth D] SDF format, chain O [auth A] SDF format, chain OC [auth F] SDF format, chain QB [auth D] SDF format, chain BC [auth E] SDF format, chain CC [auth E] SDF format, chain DA [auth B] SDF format, chain NC [auth F] SDF format, chain OB [auth D] SDF format, chain PB [auth D] MOL2 format, chain DC [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain EC [auth E] MOL2 format, chain FA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OC [auth F] MOL2 format, chain QB [auth D] MOL2 format, chain BC [auth E] MOL2 format, chain CC [auth E] MOL2 format, chain DA [auth B] MOL2 format, chain NC [auth F] MOL2 format, chain OB [auth D] MOL2 format, chain PB [auth D]	BC [auth E], CC [auth E], DA [auth B], DC [auth E], EA [auth B], 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		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain Z [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain KB [auth D] SDF format, chain TA [auth C] SDF format, chain XB [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain TA [auth C] MOL2 format, chain XB [auth E]	G [auth A], H [auth A], I [auth A], J [auth A], KB [auth D], 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		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AC [auth E] SDF format, chain CA [auth B] SDF format, chain L [auth A] SDF format, chain MB [auth D] SDF format, chain MC [auth F] SDF format, chain UA [auth C] SDF format, chain ZB [auth E] SDF format, chain BA [auth B] SDF format, chain LB [auth D] SDF format, chain LC [auth F] SDF format, chain M [auth A] SDF format, chain VA [auth C] MOL2 format, chain AC [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain MC [auth F] MOL2 format, chain UA [auth C] MOL2 format, chain ZB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain LB [auth D] MOL2 format, chain LC [auth F] MOL2 format, chain M [auth A] MOL2 format, chain VA [auth C]	AC [auth E], BA [auth B], CA [auth B], L [auth A], LB [auth D], 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		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain YB [auth E] SDF format, chain AA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain YB [auth E] MOL2 format, chain AA [auth B]	AA [auth B], K [auth A], YB [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.166
R-Value Work: 0.139
R-Value Observed: 0.141
Space Group: P 1 2₁ 1
Diffraction Data DOI: 10.18430/m36nfp Protein Diffraction

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-01-02

Deposition Author(s):

Satchell, K.J.F.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2019-01-02
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.