6LDN | pdb_00006ldn

Crystal structure of T.onnurineus Csm5

PDB DOI: https://doi.org/10.2210/pdb6LDN/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Thermococcus onnurineus NA1
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpGUT1
Mutation(s): No

Deposited: 2019-11-22 Released: 2020-11-25
Deposition Author(s): Park, K.H., Woo, E.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.263 (Depositor), 0.260 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Csm5 subunit of the Type III-A Csm complex at 2.6 Angstroms resolution

Park, K.H., Woo, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 45.26 kDa
Atom Count: 2,997
Modeled Residue Count: 368
Deposited Residue Count: 397
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csm5	A	397	Thermococcus onnurineus NA1	Mutation(s): 0 Gene Names: TON_0897
UniProt
Find proteins for B6YWC2 (Thermococcus onnurineus (strain NA1)) Explore B6YWC2 Go to UniProtKB: B6YWC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B6YWC2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.263 (Depositor), 0.260 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.473	α = 90
b = 131.072	β = 90
c = 51.913	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-11-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-11-25
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Database references, Structure summary

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.