5Y9I | pdb_00005y9i

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5Y9I

Ligand Structure Quality Assessment 


This is version 1.2 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: 36.91 kDa 
  • Atom Count: 2,825 
  • Modeled Residue Count: 297 
  • Deposited Residue Count: 318 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BOG

Query on BOG


Download:Ideal Coordinates CCD File
D [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT

Query on ACT


Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CO

Query on CO


Download:Ideal Coordinates CCD File
C [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.263α = 90
b = 59.566β = 90
c = 116.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Structure summary