5ODN | pdb_00005odn

Salinibacter ruber Single-Strand Binding protein

PDB DOI: https://doi.org/10.2210/pdb5ODN/pdb
NAKB: 5ODN

Classification: DNA BINDING PROTEIN
Organism(s): Salinibacter ruber DSM 13855, Salinibacter ruber
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-07-06 Released: 2018-08-01
Deposition Author(s): Pierechod, M., Rothweiler, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.243 (Depositor), 0.245 (DCC)
R-Value Work:
0.190 (Depositor), 0.193 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5ODN

This is version 1.3 of the entry. See complete history.

Literature

Salinibacter ruber Single-Strand Binding protein

Pierechod, M., Rothweiler, U.

To be published.

Macromolecule Content

Total Structure Weight: 183.98 kDa
Atom Count: 7,084
Modeled Residue Count: 854
Deposited Residue Count: 1,598
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A, B, C, D, E A, B, C, D, E, F, G, H	196	Salinibacter ruber DSM 13855	Mutation(s): 0 Gene Names: ssb, SRU_0523
UniProt
Find proteins for Q2S565 (Salinibacter ruber (strain DSM 13855 / M31)) Explore Q2S565 Go to UniProtKB: Q2S565
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2S565
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(PTPTPTPT)-3')	I J [auth M] K [auth J] L [auth K] M [auth N] I, J [auth M], K [auth J], L [auth K], M [auth N], O [auth Q]	4	Salinibacter ruber
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA (5'-D(TPTP*T)-3')	N [auth P], P [auth L]	3	Salinibacter ruber
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.243 (Depositor), 0.245 (DCC)
R-Value Work: 0.190 (Depositor), 0.193 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.47	α = 90
b = 123.5	β = 90
c = 205.25	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-08-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-08-01
Type: Initial release
Version 1.1: 2020-12-23
Changes: Database references
Version 1.2: 2021-02-03
Changes: Database references
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description

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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.