7EDB | pdb_00007edb

EcoT38I restriction endonuclease complexed with DNA

PDB DOI: https://doi.org/10.2210/pdb7EDB/pdb
NAKB: 7EDB

Classification: DNA BINDING PROTEIN
Organism(s): Peduovirus P2, Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-03-15 Released: 2022-03-16
Deposition Author(s): Kita, K., Mikami, B.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.197 (Depositor), 0.197 (DCC)
R-Value Work:
0.162 (Depositor), 0.163 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural analysis of EcoT38I restriction endonuclease

Kita, K., Mikami, B.

To be published.

Macromolecule Content

Total Structure Weight: 87.46 kDa
Atom Count: 6,405
Modeled Residue Count: 722
Deposited Residue Count: 728
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EcoT38I restriction endonuclease	A, B	351	Peduovirus P2	Mutation(s): 0 Gene Names: ecoT38IR
UniProt
Find proteins for Q83VS8 (Peduovirus P2) Explore Q83VS8 Go to UniProtKB: Q83VS8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83VS8
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(GPGPCPAPGPAPGPCPTPCPAPCP*G)-3')	C [auth E]	13	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(PCPGPTPGPAPGPCPTPCPTPGPC)-3')	D [auth F]	13	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE (Subject of Investigation/LOI) Query on PGE Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
TRS (Subject of Investigation/LOI) Query on TRS Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], Q [auth B], R [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain V [auth E] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain V [auth E] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] S [auth B] I [auth A], J [auth A], K [auth A], L [auth A], S [auth B], T [auth B], U [auth B], V [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth E] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth E]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain N [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain W [auth F] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain W [auth F] mmCIF format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], N [auth B], W [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain W [auth F] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain W [auth F]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain M [auth A] MOL2 format, chain X [auth F] MOL2 format, chain M [auth A] mmCIF format, chain X [auth F] mmCIF format, chain M [auth A]	M [auth A], X [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain X [auth F] Interactions & Density Focus chain M [auth A] Focus chain X [auth F]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]