8DJQ

Sliding-clamp-DnaE1 peptide

• PDB DOI: https://doi.org/10.2210/pdb8DJQ/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycolicibacterium thermoresistibile ATCC 19527, Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-01 Released: 2023-01-18 
• Deposition Author(s): Kapur, M.K., Gray, O.J., Honzatko, R.H., Nelson, S.N.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

Literature

Interaction of the sliding clamp with mycobacterial polymerases

Kapur, M.K., Gray, O.J., Honzatko, R.H., Nelson, S.N.

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.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 169.85 kDa 
• Atom Count: 12,265 
• Modelled Residue Count: 1,571 
• Deposited Residue Count: 1,612 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A, B, E [auth C], F [auth D]	397	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 0  Gene Names: KEK_10778
UniProt
Find proteins for G7CIP4 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CIP4  Go to UniProtKB:  G7CIP4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit alpha peptide	C [auth E], D [auth F], G, H	6	Mycobacterium tuberculosis	Mutation(s): 0  EC: 2.7.7.7
UniProt
Find proteins for P9WNT7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNT7  Go to UniProtKB:  P9WNT7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACE (Subject of Investigation/LOI)	I [auth E], K [auth F], M [auth G], O [auth H]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N
NH2 (Subject of Investigation/LOI)	J [auth E], L [auth F], N [auth G], P [auth H]	AMINO GROUP H2 N QGZKDVFQNNGYKY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.81	α = 90
b = 148.252	β = 92.183
c = 81.952	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Kapur, M.K., Gray, O.J., Honzatko, R.H., Nelson, S.N.

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Funding Organization	Location	Grant Number
Other government	United States	--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description