5WWM | pdb_00005wwm

Crystal structure of the TPR domain of Rrp5

PDB DOI: https://doi.org/10.2210/pdb5WWM/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-01-03 Released: 2017-01-25
Deposition Author(s): Ye, K., Chen, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.205 (Depositor), 0.200 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Correction: Molecular architecture of the 90S small subunit pre-ribosome

Sun, Q., Zhu, X., Qi, J., An, W., Lan, P., Tan, D., Chen, R., Wang, B., Zheng, S., Zhang, C., Chen, X., Zhang, W., Chen, J., Dong, M.Q., Ye, K.

(2017) Elife 6

PubMed: 28649947 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.7554/eLife.29876
Primary Citation Related Structures:
5WWM

Macromolecule Content

Total Structure Weight: 38.76 kDa
Atom Count: 2,249
Modeled Residue Count: 272
Deposited Residue Count: 331
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA biogenesis protein RRP5	A	331	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RRP5, FMI1, YMR229C, YM9959.11C
UniProt
Find proteins for Q05022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05022 Go to UniProtKB: Q05022
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05022
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.205 (Depositor), 0.200 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.526	α = 90
b = 114.526	β = 90
c = 70.933	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
DENZO	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2017-11-01
Changes: Database references
Version 1.2: 2024-03-20
Changes: Data collection, Database references

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.