6P81 | pdb_00006p81

Structure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella pneumoniae, expressed with an N-terminal His-Smt3 fusion tag, in complex with Griselimycin

• PDB DOI: https://doi.org/10.2210/pdb6P81/pdb

• Classification: Transferase/Antibiotic
• Organism(s): Saccharomyces cerevisiae S288C, Klebsiella pneumoniae IS22, Streptomyces muensis
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-06-06 Released: 2019-07-10 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Structure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella pneumoniae, expressed with an N-terminal His-Smt3 fusion tag, in complex with Griselimycin

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.16 kDa 
• Atom Count: 3,949 
• Modeled Residue Count: 451 
• Deposited Residue Count: 473 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3,Beta sliding clamp	A	462	Saccharomyces cerevisiae S288C, Klebsiella pneumoniae IS22 This entity is chimeric	Mutation(s): 0  Gene Names: SMT3, YDR510W, D9719.15
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306  Go to UniProtKB:  Q12306

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Griselimycin	B	11	Streptomyces muensis	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG5	D [auth A]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C8 H18 O4 YFNKIDBQEZZDLK-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36p81

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.02	α = 90
b = 83.1	β = 90
c = 188.18	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PARROT	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-07-10
  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