7R4W | pdb_00007r4w

Single stranded DNA binding protein SSB M5 from Fervidobacterium gondwanense

PDB DOI: https://doi.org/10.2210/pdb7R4W/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Fervidobacterium gondwanense
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-02-09 Released: 2023-08-23
Deposition Author(s): Hakansson, M., Svensson, L.A., Werbowy, O., Al-Karadaghi, S., Kaczorowski, T., Kaczorowska, A.K., Dorawa, S.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.255 (Depositor), 0.260 (DCC)
R-Value Work:
0.187 (Depositor), 0.194 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Molecular characterization of a single stranded DNA binding protein from Fervidobacterium gondwanense

Werbowy, O., Hakansson, M., Svensson, L.A., Al-Karadaghi, S., Kaczorowski, T., Kaczarowska, A.K., Dorawa, S.

To be published.

Macromolecule Content

Total Structure Weight: 17 kDa
Atom Count: 826
Modeled Residue Count: 100
Deposited Residue Count: 145
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A	145	Fervidobacterium gondwanense	Mutation(s): 0 Gene Names: SAMN02745226_00543
UniProt
Find proteins for A0A1M7S684 (Fervidobacterium gondwanense DSM 13020) Explore A0A1M7S684 Go to UniProtKB: A0A1M7S684
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1M7S684
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.255 (Depositor), 0.260 (DCC)
R-Value Work: 0.187 (Depositor), 0.194 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.39	α = 90
b = 62.39	β = 90
c = 172.38	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MrBUMP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-23

Deposition Author(s):

Al-Karadaghi, S.

Kaczorowski, T.

Kaczorowska, A.K.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	685778

Revision History (Full details and data files)

Version 1.0: 2023-08-23
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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.