6PTV

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

• PDB DOI: https://doi.org/10.2210/pdb6PTV/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Rickettsia rickettsii str. 'Sheila Smith, Streptomyces griseus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-16 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: 1.85 Å
• R-Value Free: 0.206 
• R-Value Work: 0.169 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Rickettsia rickettsii 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: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 175.97 kDa 
• Atom Count: 13,188 
• Modelled Residue Count: 1,533 
• Deposited Residue Count: 1,570 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A, B, D [auth C], F [auth D]	387	Rickettsia rickettsii str. 'Sheila Smith	Mutation(s): 0  Gene Names: A1G_03290
UniProt
Find proteins for A0A0H3AWV3 (Rickettsia rickettsii (strain Sheila Smith)) Explore A0A0H3AWV3  Go to UniProtKB:  A0A0H3AWV3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY	C [auth X], E [auth Y]	11	Streptomyces griseus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	G [auth A], H [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.206 
• R-Value Work: 0.169 
• R-Value Observed: 0.169 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M36PTV

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.21	α = 109.38
b = 82.79	β = 89.94
c = 82.86	γ = 106.53

Software Package:

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

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: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection, Derived calculations