8D8M | pdb_00008d8m

Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence grown in a calcium chloride crystallization solution.

• PDB DOI: https://doi.org/10.2210/pdb8D8M/pdb
• NAKB: 8D8M

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Escherichia coli, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-06-08 Released: 2023-06-28 
• Deposition Author(s): Orun, A.R., Snow, C.D.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Designed crystalline assemblies of protein and DNA enable site-specific installation of a guest protein, DNA, and small molecule.

Orun, A.R., Shields, E.T., Dmytriw, S., Vajapayajula, A., Snow, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 50.52 kDa 
• Atom Count: 3,065 
• Modeled Residue Count: 274 
• Deposited Residue Count: 327 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication initiation protein	C	263	Escherichia coli K-12	Mutation(s): 1  Gene Names: repE, E, rep, ECOK12F045
UniProt
Find proteins for P03856 (Escherichia coli (strain K12)) Explore P03856  Go to UniProtKB:  P03856

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CP*CP*CP*GP*GP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*AP*CP*GP*GP*A)-3')	A	32	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GP*CP*CP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*TP*CP*CP*GP*GP*A)-3')	B	32	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.322	α = 90
b = 133.189	β = 90
c = 134.645	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): Orun, A.R., Snow, C.D.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2003748

Revision History  

• Version 1.0: 2023-06-28
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description