5W7Z | pdb_00005w7z

Crystal structure of DNA polymerase III subunit beta from Rickettsia conorii

• PDB DOI: https://doi.org/10.2210/pdb5W7Z/pdb

• Classification: TRANSFERASE
• Organism(s): Rickettsia conorii str. Malish 7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-21 Released: 2017-07-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DNA polymerase III subunit beta from Rickettsia conorii

Bowatte, K., Conrady, D.G., Abendroth, J., 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 86.93 kDa 
• Atom Count: 6,962 
• Modeled Residue Count: 761 
• Deposited Residue Count: 774 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit beta	A, B	387	Rickettsia conorii str. Malish 7	Mutation(s): 0  Gene Names: dnaN, RC0583 EC: 2.7.7.7
UniProt
Find proteins for Q92I37 (Rickettsia conorii (strain ATCC VR-613 / Malish 7)) Explore Q92I37  Go to UniProtKB:  Q92I37

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	E [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
EDO	C [auth A], D [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35W7Z

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.52	α = 90
b = 86.91	β = 115.39
c = 79.51	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-07-26
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Derived calculations
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description