9F7L

Bartonella henselae NrnC bound to deoxy-pGG

PDB DOI: https://doi.org/10.2210/pdb9F7L/pdb
NAKB: 9F7L

Classification: HYDROLASE
Organism(s): Bartonella henselae
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: 2.20 Å
R-Value Free: 0.210
R-Value Work: 0.176
R-Value Observed: 0.176

Starting Model: experimental
View more details

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: 192.94 kDa
Atom Count: 14,342
Modelled Residue Count: 1,661
Deposited Residue Count: 1,672
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
3'-5' exonuclease	A, C, E, G, I A, C, E, G, I, K, M, O	207	Bartonella henselae	Mutation(s): 0 Gene Names: BM1374165_00260
UniProt
Find proteins for X5MEI1 (Bartonella henselae) Explore X5MEI1 Go to UniProtKB: X5MEI1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	X5MEI1
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-R(PDGPDG)-3')	B, D, F, H, J B, D, F, H, J, L, N, P	2	Bartonella henselae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain W [auth C] MOL2 format, chain T [auth A] MOL2 format, chain W [auth C] mmCIF format, chain T [auth A] mmCIF format, chain W [auth C]	T [auth A], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth A] Focus chain W [auth C] Interactions & Density Focus chain T [auth A] Focus chain W [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth I] SDF format, chain DA [auth K] SDF format, chain EA [auth K] SDF format, chain FA [auth M] SDF format, chain GA [auth M] SDF format, chain HA [auth O] SDF format, chain IA [auth O] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth G] SDF format, chain CA [auth I] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth I] MOL2 format, chain DA [auth K] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth M] MOL2 format, chain GA [auth M] MOL2 format, chain HA [auth O] MOL2 format, chain IA [auth O] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth G] MOL2 format, chain CA [auth I] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth I] mmCIF format, chain DA [auth K] mmCIF format, chain EA [auth K] mmCIF format, chain FA [auth M] mmCIF format, chain GA [auth M] mmCIF format, chain HA [auth O] mmCIF format, chain IA [auth O] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth G] mmCIF format, chain CA [auth I]	AA [auth G] BA [auth I] CA [auth I] DA [auth K] EA [auth K] AA [auth G], BA [auth I], CA [auth I], DA [auth K], EA [auth K], FA [auth M], GA [auth M], HA [auth O], IA [auth O], Q [auth A], R [auth A], S [auth A], U [auth C], V [auth C], X [auth E], Y [auth E], Z [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain DA [auth K] Focus chain EA [auth K] Focus chain FA [auth M] Focus chain GA [auth M] Focus chain HA [auth O] Focus chain IA [auth O] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain DA [auth K] Focus chain EA [auth K] Focus chain FA [auth M] Focus chain GA [auth M] Focus chain HA [auth O] Focus chain IA [auth O] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth G]