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), 0.251 (DCC)
R-Value Work:
0.210 (Depositor), 0.209 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.251 (DCC)
R-Value Work: 0.210 (Depositor), 0.209 (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

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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

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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.