6DLY | pdb_00006dly

Crystal structure of DNA polymerase III subunit beta from Mycobacterium marinum in complex with a natural product

• PDB DOI: https://doi.org/10.2210/pdb6DLY/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium marinum M, 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: 2.10 Å
• R-Value Free: 
  0.226 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DNA polymerase III subunit beta from Mycobacterium marinum in complex with a natural product

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: 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: 89 kDa 
• Atom Count: 6,124 
• Modeled Residue Count: 781 
• Deposited Residue Count: 842 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A, B	410	Mycobacterium marinum M	Mutation(s): 0  Gene Names: dnaN, MMAR_0002
UniProt
Find proteins for B2HI47 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HI47  Go to UniProtKB:  B2HI47

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

Small Molecules

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

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLU	C, D	D-PEPTIDE LINKING	C7 H15 N O2		--
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: 2.10 Å
• R-Value Free:  0.226 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36DLY

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.09	α = 90
b = 76.76	β = 117.53
c = 80.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
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, Source and taxonomy, 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