9F7M

Blastococcus Orn bound to pGG

PDB DOI: https://doi.org/10.2210/pdb9F7M/pdb
NAKB: 9F7M

Classification: HYDROLASE
Organism(s): Blastococcus aggregatus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-04 Released: 2024-12-04
Deposition Author(s): Mortensen, S., Sondermann, H.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.191
R-Value Work: 0.171
R-Value Observed: 0.171

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Unique dinucleases with DNA specificity are associated with genomic islands in Actinomycetes and Clostridia

Mortensen, S., Sondermann, H.

To be published.

Macromolecule Content

Total Structure Weight: 196.86 kDa
Atom Count: 15,031
Modelled Residue Count: 1,668
Deposited Residue Count: 1,768
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligoribonuclease	A C [auth B] E [auth C] G [auth D] I [auth E] A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	219	Blastococcus aggregatus	Mutation(s): 0 Gene Names: orn, SAMN05660748_0160 EC: 3.1
UniProt
Find proteins for A0A285UWY4 (Blastococcus aggregatus) Explore A0A285UWY4 Go to UniProtKB: A0A285UWY4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A285UWY4
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(PGPG)-3')	B [auth I] D [auth J] F [auth K] H [auth L] J [auth M] B [auth I], D [auth J], F [auth K], H [auth L], J [auth M], L [auth N], N [auth O], P	2	Blastococcus aggregatus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth I] SDF format, chain S [auth J] SDF format, chain T [auth C] SDF format, chain U [auth K] SDF format, chain V [auth L] SDF format, chain W [auth M] SDF format, chain X [auth N] SDF format, chain Y [auth O] SDF format, chain Z [auth P] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth I] MOL2 format, chain S [auth J] MOL2 format, chain T [auth C] MOL2 format, chain U [auth K] MOL2 format, chain V [auth L] MOL2 format, chain W [auth M] MOL2 format, chain X [auth N] MOL2 format, chain Y [auth O] MOL2 format, chain Z [auth P] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth I] mmCIF format, chain S [auth J] mmCIF format, chain T [auth C] mmCIF format, chain U [auth K] mmCIF format, chain V [auth L] mmCIF format, chain W [auth M] mmCIF format, chain X [auth N] mmCIF format, chain Y [auth O] mmCIF format, chain Z [auth P]	Q [auth A] R [auth I] S [auth J] T [auth C] U [auth K] Q [auth A], R [auth I], S [auth J], T [auth C], U [auth K], V [auth L], W [auth M], X [auth N], Y [auth O], Z [auth P]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth I] Focus chain S [auth J] Focus chain T [auth C] Focus chain U [auth K] Focus chain V [auth L] Focus chain W [auth M] Focus chain X [auth N] Focus chain Y [auth O] Focus chain Z [auth P] Interactions & Density Focus chain Q [auth A] Focus chain R [auth I] Focus chain S [auth J] Focus chain T [auth C] Focus chain U [auth K] Focus chain V [auth L] Focus chain W [auth M] Focus chain X [auth N] Focus chain Y [auth O] Focus chain Z [auth P]