5Y9Y | pdb_00005y9y

Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with succinate and Co(II)

PDB DOI: https://doi.org/10.2210/pdb5Y9Y/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Methylacidiphilum infernorum V4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-29 Released: 2018-10-31
Deposition Author(s): Chung, H.S., Pemble, C.W., Joo, S.H., Raetz, C.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.194 (Depositor), 0.187 (DCC)
R-Value Work:
0.159 (Depositor), 0.159 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5Y9Y

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

Literature

Biochemical and structural insights of Fe(II)/alpha-ketoglutarate/O2-dependent dioxygenase, KdoO from Methylacidiphilum infernorum V4

Chung, H.S., Pemble IV, C.W., Joo, S.H.

To be published.

Macromolecule Content

Total Structure Weight: 37.94 kDa
Atom Count: 2,743
Modeled Residue Count: 297
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein KdoO	A	318	Methylacidiphilum infernorum V4	Mutation(s): 0 Gene Names: Minf_1012
UniProt
Find proteins for B3DUR4 (Methylacidiphilum infernorum (isolate V4)) Explore B3DUR4 Go to UniProtKB: B3DUR4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3DUR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	N [auth A], O [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	J [auth A], K [auth A], L [auth A], M [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.194 (Depositor), 0.187 (DCC)
R-Value Work: 0.159 (Depositor), 0.159 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.762	α = 90
b = 59.316	β = 90
c = 116.429	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-10-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-10-31
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references, Derived calculations

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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.