3OBZ | pdb_00003obz

Crystal structure of human phytanoyl-COA dioxygenase phyhd1 2-oxoglutarate and iron complex

• PDB DOI: https://doi.org/10.2210/pdb3OBZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-09 Released: 2010-09-01 
• Deposition Author(s): Zhang, Z., McDonough, M.A., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.274 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.242 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of Human PHYHD1, a Non-Heme Fe(II) and 2-Oxoglutarate Dependent Oxygenase Related to Phytanoyl-CoA Hydroxylase

Zhang, Z., Butler, D., McDonough, M.A., Kavanagh, K.L., Bray, J.E., Ng, S.S., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Schofield, C.J., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.65 kDa 
• Atom Count: 2,478 
• Modeled Residue Count: 290 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytanoyl-CoA dioxygenase domain-containing protein 1	A	291	Homo sapiens	Mutation(s): 0  Gene Names: PHYHD1 EC: 1 (PDB Primary Data), 1.14.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SRE7 (Homo sapiens) Explore Q5SRE7  Go to UniProtKB:  Q5SRE7
PHAROS:  Q5SRE7 GTEx:  ENSG00000175287

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	B [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE2	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.274 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.242 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.366	α = 90
b = 92.366	β = 90
c = 81.754	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Zhang, Z., McDonough, M.A., Schofield, C.J.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description