9K30 | pdb_00009k30

Classification: RNA BINDING PROTEIN
Organism(s): Tissierellia bacterium, synthetic construct
Expression System: Escherichia coli, Cloning vector pCOLA-AraC-pBAD-lacI-LVA-TetR-LVA
Mutation(s): No

Deposited: 2024-10-18 Released: 2026-02-04
Deposition Author(s): Nagahata, N., Yamada, S., Yamashita, K., Nishimasu, H.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Nagahata, N.

To be published.

Macromolecule Content

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TbaIscB	A	1,068	Tissierellia bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
Omega RNA	B	443	Tissierellia bacterium
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
Target DNA strand	C	43	synthetic construct
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
Non-target DNA strand	D	43	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Servalcat
RECONSTRUCTION	cryoSPARC

Entry History & Funding Information

Deposition Author(s):

Nagahata, N.

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR23B6
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H05281
Japan Society for the Promotion of Science (JSPS)	Japan	JP22H00403