5Y9X

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 

wwPDB Validation   3D Report Full Report


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein KdoO318Methylacidiphilum infernorum V4Mutation(s): 0 
Gene Names: Minf_1012
UniProt
Find proteins for B3DUR4 (Methylacidiphilum infernorum (isolate V4))
Explore B3DUR4 
Go to UniProtKB:  B3DUR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3DUR4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

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D [auth A],
E [auth A],
F [auth A],
G [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
AKG
Query on AKG

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C [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
SO4
Query on SO4

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H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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Q [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

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K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CO
Query on CO

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B [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
CL
Query on CL

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R [auth A],
S [auth A],
T [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.038α = 90
b = 59.263β = 90
c = 116.253γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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