8PNK

Crystal structure of the Ded1p RecA1 domain

PDB DOI: https://doi.org/10.2210/pdb8PNK/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-30 Released: 2023-08-16
Deposition Author(s): Huebner, J., Sprangers, R.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the Ded1p RecA1 domain

Huebner, J., Sprangers, R.

To be published.

Macromolecule Content

Total Structure Weight: 31.8 kDa
Atom Count: 2,026
Modelled Residue Count: 256
Deposited Residue Count: 289
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DED1	A	289	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: DED1, SPP81, YOR204W EC: 3.6.4.13
UniProt
Find proteins for P06634 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06634 Go to UniProtKB: P06634
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06634
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.225 (Depositor), 0.220 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110	α = 90
b = 110	β = 90
c = 52.2	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	418960343

Revision History (Full details and data files)

Version 1.0: 2023-08-16
Type: Initial release

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.