3KBG | pdb_00003kbg

Crystal structure of the 30S ribosomal protein S4e from Thermoplasma acidophilum. Northeast Structural Genomics Consortium Target TaR28.

PDB DOI: https://doi.org/10.2210/pdb3KBG/pdb

Classification: RIBOSOMAL PROTEIN
Organism(s): Thermoplasma acidophilum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2009-10-20 Released: 2009-10-27
Deposition Author(s): Vorobiev, S.M., Su, M., Seetharaman, J., Belote, R.L., Ciccosanti, C., Patel, D., Liu, J., Rost, B., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.217 (Depositor), 0.218 (DCC)
R-Value Work:
0.184 (Depositor), 0.186 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3KBG

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the 30S ribosomal protein S4e from Thermoplasma acidophilum.

Vorobiev, S.M., Su, M., Seetharaman, J., Belote, R.L., Ciccosanti, C., Liu, J., Rost, B., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 24.08 kDa
Atom Count: 1,666
Modeled Residue Count: 192
Deposited Residue Count: 213
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4e	A	213	Thermoplasma acidophilum	Mutation(s): 2 Gene Names: rps4e, Ta1259
UniProt
Find proteins for Q56230 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q56230 Go to UniProtKB: Q56230
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q56230
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.217 (Depositor), 0.218 (DCC)
R-Value Work: 0.184 (Depositor), 0.186 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.831	α = 90
b = 74.831	β = 90
c = 64.133	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SnB	phasing
RESOLVE	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-10-27

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2024-11-27
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.