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), 0.262 (DCC)
R-Value Work:
0.208 (Depositor), 0.208 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6LDN

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.262 (DCC)
R-Value Work: 0.208 (Depositor), 0.208 (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

View more in-depth experimental data

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 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.