3MGU | pdb_00003mgu

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.296 (Depositor), 0.281 (DCC)
R-Value Work:
0.239 (Depositor), 0.232 (DCC)
R-Value Observed:
0.242 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40032
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.296 (Depositor), 0.281 (DCC)
R-Value Work: 0.239 (Depositor), 0.232 (DCC)
R-Value Observed: 0.242 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

van Tilbeurgh, H.

Revision History (Full details and data files)

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
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.