2OPW | pdb_00002opw

Crystal structure of human phytanoyl-CoA dioxygenase PHYHD1 (apo)

• PDB DOI: https://doi.org/10.2210/pdb2OPW/pdb

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


• Deposited: 2007-01-30 Released: 2007-03-06 
• Deposition Author(s): 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., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.258 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human phytanoyl-CoA dioxygenase PHYHD1 (apo)

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: 32.45 kDa 
• Atom Count: 2,333 
• Modeled Residue Count: 286 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.258 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.97	α = 90
b = 91.97	β = 90
c = 81.61	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): 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., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-06-27
  Changes: Data collection, Derived calculations
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references
• Version 1.6: 2024-04-03
  Changes: Refinement description
• Version 1.7: 2024-11-13
  Changes: Structure summary