3MGU

Structure of S. cerevisiae Tpa1 protein, a proline hydroxylase modifying ribosomal protein Rps23

• PDB DOI: https://doi.org/10.2210/pdb3MGU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-04-07 Released: 2010-07-14 
• Deposition Author(s): Henri, J., Rispal, D., Bayart, E., van Tilbeurgh, H., Seraphin, B., Graille, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.296 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 

Literature

Structural and functional insights into S. cerevisiae Tpa1, a putative prolyl hydroxylase influencing translation termination and transcription

Henri, J., Rispal, D., Bayart, E., van Tilbeurgh, H., Seraphin, B., Graille, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.2 kDa 
• Atom Count: 4,406 
• Modelled Residue Count: 533 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PKHD-type hydroxylase TPA1	A	644	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: TPA1, YER049W EC: 1.14.11
UniProt
Find proteins for P40032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40032  Go to UniProtKB:  P40032

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.296 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.18	α = 90
b = 104.84	β = 90
c = 205.57	γ = 90

Software Package:

Software Name	Purpose
MX	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Henri, J., Rispal, D., Bayart, E., van Tilbeurgh, H., Seraphin, B., Graille, M.

Revision History  

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-03
  Changes: Structure summary