7QTF | pdb_00007qtf

Crystal Structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase PlaO1 in complex with sodium succinate

PDB DOI: https://doi.org/10.2210/pdb7QTF/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces sp. Tu6071
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-14 Released: 2023-01-18
Deposition Author(s): Lukat, P., Daum, M., Bechthold, A., Einsle, O.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.173 (Depositor), 0.173 (DCC)
R-Value Work:
0.150 (Depositor), 0.151 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural investigations on the Fe(II)/alpha-ketoglutarate dependent dioxygense PlaO1 from Streptomyces sp. Tu6071

Lukat, P.

(2011) Thesis

Macromolecule Content

Total Structure Weight: 136.22 kDa
Atom Count: 10,393
Modeled Residue Count: 1,117
Deposited Residue Count: 1,188
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PlaO1	A, B, C, D	297	Streptomyces sp. Tu6071	Mutation(s): 0 Gene Names: plaO1, STTU_1451
UniProt
Find proteins for Q2I752 (Streptomyces sp. Tu6071) Explore Q2I752 Go to UniProtKB: Q2I752
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2I752
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIN (Subject of Investigation/LOI) Query on SIN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	F [auth A], I [auth B], L [auth C], N [auth D]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth C]	E [auth A], K [auth C]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	H [auth A], J [auth B], M [auth C], O [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D]