5US8 | pdb_00005us8

2.15 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis

PDB DOI: https://doi.org/10.2210/pdb5US8/pdb

Classification: HYDROLASE,OXIDOREDUCTASE
Organism(s): Bordetella pertussis Tohama I
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-13 Released: 2017-03-01
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Stam, J., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.200 (Depositor), 0.210 (DCC)
R-Value Work:
0.156 (Depositor), 0.160 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.

Macromolecule Content

Total Structure Weight: 100.52 kDa
Atom Count: 7,605
Modeled Residue Count: 890
Deposited Residue Count: 896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Argininosuccinate synthase	A, B	448	Bordetella pertussis Tohama I	Mutation(s): 0 Gene Names: argG, BP3537 EC: 6.3.4.5
UniProt
Find proteins for Q7VTJ9 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VTJ9 Go to UniProtKB: Q7VTJ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7VTJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADN Query on ADN Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], E [auth B], F [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.200 (Depositor), 0.210 (DCC)
R-Value Work: 0.156 (Depositor), 0.160 (DCC)
R-Value Observed: 0.158 (Depositor)

Diffraction Data: https://doi.org/10.18430/m35us8

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.453	α = 90
b = 94.453	β = 90
c = 188.49	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-03-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-03-01
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2026-02-11
Changes: Database references, Structure summary