6DM6 | pdb_00006dm6

Structure of DNA polymerase III subunit beta from Rickettsia conorii in complex with a natural product

• PDB DOI: https://doi.org/10.2210/pdb6DM6/pdb

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


• Deposited: 2018-06-04 Released: 2019-06-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure of DNA polymerase III subunit beta from Rickettsia conorii in complex with a natural product

Conrady, D.G., Abendroth, J., Higgins, T.W., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.86 kDa 
• Atom Count: 6,210 
• Modeled Residue Count: 777 
• Deposited Residue Count: 796 
• Unique protein chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Natural product peptide	C, D	11	Streptomyces muensis	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MP8	C, D	L-PEPTIDE LINKING	C6 H11 N O2		PRO
MVA	C, D	L-PEPTIDE LINKING	C6 H13 N O2		VAL
NZC	C, D	L-PEPTIDE LINKING	C5 H11 N O3		THR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002311	C, D	ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36DM6

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.86	α = 90
b = 41.83	β = 93.92
c = 127.4	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection, Derived calculations