6NFP

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)

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 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.

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

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

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

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):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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