6IRQ | pdb_00006irq

Complexed crystal structure of PaSSB with ssDNA dT25 at 1.91 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6IRQ/pdb
NAKB: 6IRQ

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Pseudomonas aeruginosa PAO1, synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2018-11-14 Released: 2019-12-11
Deposition Author(s): Huang, Y.H., Huang, C.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.246 (Depositor)
R-Value Work:
0.213 (Depositor)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6IRQ

This is version 1.2 of the entry. See complete history.

Literature

Characterization of an SSB-dT25 complex: structural insights into the S-shaped ssDNA binding conformation.

Huang, Y.H., Chen, I.C., Huang, C.Y.

(2019) RSC Adv 9: 40388-40396

DOI: https://doi.org/10.1039/C9RA09406G

Macromolecule Content

Total Structure Weight: 70.22 kDa
Atom Count: 3,881
Modeled Residue Count: 437
Deposited Residue Count: 534
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A, B, C, D	121	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: ssb, PA4232
UniProt
Find proteins for P40947 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P40947 Go to UniProtKB: P40947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40947
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (25-MER)	E, F	25	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.246 (Depositor)
R-Value Work: 0.213 (Depositor)
R-Value Observed: 0.215 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.488	α = 90
b = 60.488	β = 90
c = 131.315	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-12-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-12-11
Type: Initial release
Version 1.1: 2020-06-24
Changes: Database references
Version 1.2: 2023-11-22
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.