6NBK | pdb_00006nbk

Crystal structure of Arginase from Bacillus cereus

PDB DOI: https://doi.org/10.2210/pdb6NBK/pdb

Classification: HYDROLASE
Organism(s): Bacillus thuringiensis DB27
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-07 Released: 2018-12-19
Deposition Author(s): Chang, C., Evdokimova, E., Mcchesney, M., Joachimiak, A., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.203 (Depositor), 0.200 (DCC)
R-Value Work:
0.161 (Depositor), 0.160 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Arginase from Bacillus cereus

Chang, C., Evdokimova, E., Mcchesney, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 194.99 kDa
Atom Count: 14,725
Modeled Residue Count: 1,726
Deposited Residue Count: 1,782
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	297	Bacillus thuringiensis DB27	Mutation(s): 0 Gene Names: BTDB27_005763 EC: 3.5.3.1
UniProt
Find proteins for W8YSI5 (Bacillus thuringiensis DB27) Explore W8YSI5 Go to UniProtKB: W8YSI5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W8YSI5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN 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 K [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain W [auth F] SDF format, chain S [auth D] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] MOL2 format, chain S [auth D] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F] mmCIF format, chain S [auth D] mmCIF format, chain L [auth B]	G [auth A] H [auth A] I [auth A] K [auth B] L [auth B] G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], R [auth D], S [auth D], T [auth E], U [auth E], V [auth F], W [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C]	J [auth A], N [auth B], Q [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.203 (Depositor), 0.200 (DCC)
R-Value Work: 0.161 (Depositor), 0.160 (DCC)
R-Value Observed: 0.163 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36nbk

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.022	α = 90
b = 153.803	β = 90
c = 83.137	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-12-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-12-19
Type: Initial release
Version 1.1: 2019-05-15
Changes: Data collection, Experimental preparation
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary