8DKD | pdb_00008dkd

Sliding clamp from M. thermoresistibile

• PDB DOI: https://doi.org/10.2210/pdb8DKD/pdb

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


• Deposited: 2022-07-05 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: 3.20 Å
• R-Value Free: 
  0.277 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

Interaction of 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: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 41.68 kDa 
• Atom Count: 2,956 
• Modeled Residue Count: 393 
• Deposited Residue Count: 397 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.277 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.408	α = 90
b = 102.408	β = 90
c = 134.159	γ = 120

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: 2023-02-15
  Changes: Derived calculations
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description