2YWQ

Crystal structure of Thermus thermophilus Protein Y N-terminal domain

PDB DOI: https://doi.org/10.2210/pdb2YWQ/pdb

Classification: RIBOSOMAL PROTEIN
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-21 Released: 2008-04-15
Deposition Author(s): Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Saito, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.294
R-Value Work: 0.238
R-Value Observed: 0.238

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Thermus thermophilus Protein Y N-terminal domain

Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Saito, Y., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 49.02 kDa
Atom Count: 2,908
Modelled Residue Count: 357
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal subunit interface protein	A, B, C, D	105	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: TTHA1294
UniProt
Find proteins for Q5SIS0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIS0 Go to UniProtKB: Q5SIS0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SIS0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.294
R-Value Work: 0.238
R-Value Observed: 0.238
Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.774	α = 90
b = 81.774	β = 90
c = 136.553	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-04-15

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-04-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.