6PTH | pdb_00006pth

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Pseudomonas aeruginosa bound to griselimycin

• PDB DOI: https://doi.org/10.2210/pdb6PTH/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Pseudomonas aeruginosa PAO1, Streptomyces griseus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-15 Released: 2019-08-07 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Pseudomonas aeruginosa bound to griselimycin

Edwards, T.E., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.06 kDa 
• Atom Count: 2,858 
• Modeled Residue Count: 380 
• Deposited Residue Count: 474 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A	463	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: dnaN, PA0002
UniProt
Find proteins for Q9I7C4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I7C4  Go to UniProtKB:  Q9I7C4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Griselimycin	B [auth G]	11	Streptomyces griseus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLU	B [auth G]	D-PEPTIDE LINKING	C7 H15 N O2		--
MP8	B [auth G]	L-PEPTIDE LINKING	C6 H11 N O2		PRO
MVA	B [auth G]	L-PEPTIDE LINKING	C6 H13 N O2		VAL
NZC	B [auth G]	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	B [auth G]	ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36PTH

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.65	α = 90
b = 139.65	β = 90
c = 173.51	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2019-10-02
  Changes: Data collection, Derived calculations
• 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