9BZC | pdb_00009bzc

Cocrystal structure of Clostridium beijerinckii ZTP riboswitch with ZMP and Cs

PDB DOI: https://doi.org/10.2210/pdb9BZC/pdb
NAKB: 9BZC

Classification: RNA
Organism(s): Clostridium beijerinckii
Expression System: in vitro transcription vector pT7-TP(deltai)
Mutation(s): No

Deposited: 2024-05-24 Released: 2024-11-27
Deposition Author(s): Jones, C.P., Ferre-D'Amare, A.R.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.226 (Depositor), 0.234 (DCC)
R-Value Work:
0.195 (Depositor), 0.210 (DCC)
R-Value Observed:
0.198 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Cocrystal structure of Clostridium beijerinckii ZTP riboswitch with ZMP and Cs

Jones, C.P., Tran, B., Ferre-D'Amare, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 29.58 kDa
Atom Count: 1,886
Modeled Residue Count: 87
Deposited Residue Count: 89
Unique nucleic acid chains: 1

Macromolecules

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA (87-MER)	A	89	Clostridium beijerinckii
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMZ (Subject of Investigation/LOI) Query on AMZ 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]	AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE C₉ H₁₅ N₄ O₈ P NOTGFIUVDGNKRI-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CS (Subject of Investigation/LOI) Query on CS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.226 (Depositor), 0.234 (DCC)
R-Value Work: 0.195 (Depositor), 0.210 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.864	α = 90
b = 47.673	β = 129.26
c = 74.11	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
AutoSol	phasing
Aimless	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Ferre-D'Amare, A.R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release

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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.