6D46 | pdb_00006d46

Crystal structure of a DNA polymerase III subunit beta DnaN sliding clamp from Rickettsia typhi str. Wilmington

• PDB DOI: https://doi.org/10.2210/pdb6D46/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Rickettsia typhi str. Wilmington
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-17 Released: 2018-05-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a DNA polymerase III subunit beta DnaN sliding clamp from Rickettsia typhi str. Wilmington

Edwards, T.E., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.33 kDa 
• Atom Count: 3,071 
• Modeled Residue Count: 377 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A	389	Rickettsia typhi str. Wilmington	Mutation(s): 0  Gene Names: dnaN, RT0405
UniProt
Find proteins for Q68WW0 (Rickettsia typhi (strain ATCC VR-144 / Wilmington)) Explore Q68WW0  Go to UniProtKB:  Q68WW0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A], C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36D46

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.52	α = 90
b = 43.05	β = 121.39
c = 83.17	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2021-01-06
  Changes: Derived calculations
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description