1GD8 | pdb_00001gd8

THE CRYSTAL STRUCTURE OF BACTERIA-SPECIFIC L17 RIBOSOMAL PROTEIN.

PDB DOI: https://doi.org/10.2210/pdb1GD8/pdb

Classification: RIBOSOME
Organism(s): Thermus thermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-09-22 Released: 2001-09-22
Deposition Author(s): Vassylyev, D.G., Shirouzu, M., Wada, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.254 (Depositor), 0.250 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of the bacteria-specific L17 ribosomal protein from Thermus thermophilus.

Vassylyev, D.G., Shirouzu, M., Wada, T., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 123.75 kDa
Atom Count: 7,852
Modeled Residue Count: 945
Deposited Residue Count: 1,062
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L17	A, B, C, D, E A, B, C, D, E, F, G, H, I	118	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q9Z9H5 Go to UniProtKB: Q9Z9H5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Z9H5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.254 (Depositor), 0.250 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.239	α = 90
b = 109.239	β = 90
c = 128.841	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2001-09-22

Deposition Author(s):

Vassylyev, D.G.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2001-09-22
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-27
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.