8DT6 | pdb_00008dt6

Crystal Structure of DNA Polymerase III beta subunit from Elizabethkingia anophelis

PDB DOI: https://doi.org/10.2210/pdb8DT6/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Elizabethkingia anophelis NUHP1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-25 Released: 2022-08-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.218 (Depositor), 0.219 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)
R-Value Observed:
0.177 (Depositor)

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

Validation slider image for 8DT6

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

Literature

Crystal Structure of DNA Polymerase III beta subunit from Elizabethkingia anophelis

DeBouver, N.D., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 172.43 kDa
Atom Count: 11,930
Modeled Residue Count: 1,494
Deposited Residue Count: 1,536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A, B, C, D	384	Elizabethkingia anophelis NUHP1	Mutation(s): 0 Gene Names: BD94_1355
UniProt
Find proteins for A0A077EHW1 (Elizabethkingia anophelis NUHP1) Explore A0A077EHW1 Go to UniProtKB: A0A077EHW1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A077EHW1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A] G [auth B] H [auth B] K [auth C] L [auth C] E [auth A], G [auth B], H [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain F [auth B] MOL2 format, chain J [auth C] MOL2 format, chain F [auth B] mmCIF format, chain J [auth C] mmCIF format, chain F [auth B]	F [auth B], J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Focus chain J [auth C] Interactions & Density Focus chain F [auth B] Focus chain J [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain I [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain I [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain I [auth B]	I [auth B], Q [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain Q [auth D] Interactions & Density Focus chain I [auth B] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.218 (Depositor), 0.219 (DCC)
R-Value Work: 0.176 (Depositor), 0.176 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.41	α = 90
b = 88.01	β = 95.75
c = 100.24	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-08-10
Type: Initial release
Version 1.1: 2024-02-14
Changes: Data collection
Version 1.2: 2024-04-03
Changes: 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.