6DLK | pdb_00006dlk

Crystal structure of DNA polymerase III subunit beta from Rickettsia rickettsii

• PDB DOI: https://doi.org/10.2210/pdb6DLK/pdb

• Classification: TRANSFERASE
• Organism(s): Rickettsia rickettsii str. 'Sheila Smith
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-01 Released: 2018-10-03 
• 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: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DNA polymerase III subunit beta from Rickettsia rickettsii

Conrady, D.G., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.01 kDa 
• Atom Count: 6,314 
• Modeled Residue Count: 755 
• Deposited Residue Count: 774 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A, B	387	Rickettsia rickettsii str. 'Sheila Smith	Mutation(s): 0  Gene Names: A1G_03290
UniProt
Find proteins for A0A0H3AWV3 (Rickettsia rickettsii (strain Sheila Smith)) Explore A0A0H3AWV3  Go to UniProtKB:  A0A0H3AWV3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth B], E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36dlk

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.09	α = 90
b = 97.57	β = 90
c = 115.83	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description