9G5Z | pdb_00009g5z

Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF

PDB DOI: https://doi.org/10.2210/pdb9G5Z/pdb

Classification: TOXIN
Organism(s): Staphylococcus aureus, Lama glama
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-17 Released: 2024-07-24
Deposition Author(s): Prolic-Kalinsek, M., Haesaerts, S., Loris, R.
Funding Organization(s): Vrije Universiteit Brussel

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.43 Å
R-Value Free:
0.283 (Depositor), 0.284 (DCC)
R-Value Work:
0.244 (Depositor), 0.246 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Staphylococcus aureus MazF in complex with Nanobody 11

Prolic-Kalinsek, M., Zorzini, V., Haesaerts, S., De Bruyn, P., Loris, R.

To be published.

Macromolecule Content

Total Structure Weight: 57.54 kDa
Atom Count: 3,448
Modeled Residue Count: 460
Deposited Residue Count: 514
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease MazF	A, B	133	Staphylococcus aureus	Mutation(s): 0 Gene Names: mazF, SA1873 EC: 3.1
UniProt
Find proteins for Q2FWI8 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FWI8 Go to UniProtKB: Q2FWI8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FWI8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 11	C, D	124	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.43 Å
R-Value Free: 0.283 (Depositor), 0.284 (DCC)
R-Value Work: 0.244 (Depositor), 0.246 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.1	α = 90
b = 102.1	β = 90
c = 101.15	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Prolic-Kalinsek, M.

Funding Organization	Location	Grant Number
Vrije Universiteit Brussel	Belgium	SRP13

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release
Version 1.1: 2024-10-23
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.