7STW | pdb_00007stw

Structure of DPSL (DNA Protection in Starved Cells - Like) from Pyrococcus furiosus

PDB DOI: https://doi.org/10.2210/pdb7STW/pdb
EM Map EMD-25437: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-15 Released: 2021-12-01
Deposition Author(s): Gauvin, C.C., Waghwani, H.K., Douglas, T., Lawrence, C.M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7STW

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

Literature

Structure of DPSL (DNA Protection in Starved Cells - Like) from Pyrococcus furiosus

Ramsay, B., Wiedenheft, B., Allen, M., Gauss, G.H., Lawrence, C.M., Young, M., Douglas, T.

To be published.

Macromolecule Content

Total Structure Weight: 258.1 kDa
Atom Count: 16,829
Modeled Residue Count: 2,040
Deposited Residue Count: 2,220
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA protection during starvation protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	185	Pyrococcus furiosus	Mutation(s): 0 Gene Names: dps, PF1193 EC: 1.16
UniProt
Find proteins for Q8U1L3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1L3 Go to UniProtKB: Q8U1L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U1L3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain EA [auth J] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth E] SDF format, chain Y [auth G] SDF format, chain W [auth F] SDF format, chain S [auth D] SDF format, chain M [auth A] SDF format, chain IA [auth L] SDF format, chain GA [auth K] SDF format, chain AA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain EA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth E] MOL2 format, chain Y [auth G] MOL2 format, chain W [auth F] MOL2 format, chain S [auth D] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth L] MOL2 format, chain GA [auth K] MOL2 format, chain AA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain EA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth E] mmCIF format, chain Y [auth G] mmCIF format, chain W [auth F] mmCIF format, chain S [auth D] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth L] mmCIF format, chain GA [auth K] mmCIF format, chain AA [auth H]	AA [auth H] CA [auth I] EA [auth J] GA [auth K] IA [auth L] AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain DA [auth I] SDF format, chain FA [auth J] SDF format, chain JA [auth L] SDF format, chain N [auth A] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain V [auth E] SDF format, chain P [auth B] SDF format, chain HA [auth K] SDF format, chain BA [auth H] MOL2 format, chain DA [auth I] MOL2 format, chain FA [auth J] MOL2 format, chain JA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain V [auth E] MOL2 format, chain P [auth B] MOL2 format, chain HA [auth K] MOL2 format, chain BA [auth H] mmCIF format, chain DA [auth I] mmCIF format, chain FA [auth J] mmCIF format, chain JA [auth L] mmCIF format, chain N [auth A] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain V [auth E] mmCIF format, chain P [auth B] mmCIF format, chain HA [auth K] mmCIF format, chain BA [auth H]	BA [auth H] DA [auth I] FA [auth J] HA [auth K] JA [auth L] BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.2
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DBI-1828765

Revision History (Full details and data files)

Version 1.0: 2021-12-01
Type: Initial release
Version 1.1: 2024-06-05
Changes: Data collection, 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.