Macromolecule Content

Total Structure Weight: 65.07 kDa
Atom Count: 4804
Residue Count: 563
Unique protein chains: 1

5ZNJ

Crystal structure of a bacterial ProRS with ligands

DOI: 10.2210/pdb5ZNJ/pdb

Classification: LIGASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-09 Released: 2019-05-29
Deposition Author(s): Cheng, B., Yu, Y., Zhou, H.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.222
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Literature

Crystal structure of a bacterial ProRS with ligands

Cheng, B., Luo, S., Luo, Z., Chen, Y., Yu, Y., Guo, J., Liu, Q., Zhou, H.

To be published.

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline--tRNA ligase	A	567	Staphylococcus aureus	Mutation(s): 0 Gene Names: proS, CT123_02285 EC: 6.1.1.15
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download CCD File	A	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Ligand Interaction
HFG Query on HFG Download CCD File	A	7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one C₁₆ H₁₇ Br Cl N₃ O₃ LVASCWIMLIKXLA-CABCVRRESA-N		Ligand Interaction
PO4 Query on PO4 Download CCD File	A	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
GOL Query on GOL Download CCD File	A	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download CCD File	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.222
R-Value Work: 0.197
R-Value Observed: 0.199
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.139	α = 90
b = 77.535	β = 99.36
c = 74.226	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2018-04-09
Released Date: 2019-05-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81773636

Revision History

Version 1.0: 2019-05-29
Type: Initial release

RCSB PDB is 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.