7QTD | pdb_00007qtd

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

PDB DOI: https://doi.org/10.2210/pdb7QTD/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: 1.75 Å
R-Value Free:
0.165 (Depositor), 0.164 (DCC)
R-Value Work:
0.141 (Depositor), 0.141 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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

(2011) Thesis

Macromolecule Content

Total Structure Weight: 136.8 kDa
Atom Count: 10,544
Modeled Residue Count: 1,121
Deposited Residue Count: 1,188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKG Query on AKG Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], O [auth C], U [auth D]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain U [auth D]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain E [auth A] MOL2 format, chain S [auth C] MOL2 format, chain E [auth A] mmCIF format, chain S [auth C] mmCIF format, chain E [auth A]	E [auth A], S [auth C]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain S [auth C] Interactions & Density Focus chain E [auth A] Focus chain S [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] L [auth B] P [auth C] Q [auth C] H [auth A], I [auth A], L [auth B], P [auth C], Q [auth C], V [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D]
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain T [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain T [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], N [auth C], T [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain T [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B]	M [auth B], R [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain M [auth B] Focus chain R [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.165 (Depositor), 0.164 (DCC)
R-Value Work: 0.141 (Depositor), 0.141 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.124	α = 90
b = 108.215	β = 94.75
c = 116.408	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2023-08-16
Changes: Data collection, Database references
Version 1.2: 2024-01-31
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.