7RVA | pdb_00007rva

Updated Crystal Structure of Replication Initiator Protein REPE54.

• PDB DOI: https://doi.org/10.2210/pdb7RVA/pdb
• NAKB: 7RVA

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


• Deposited: 2021-08-18 Released: 2021-09-01 
• Deposition Author(s): Ward, A.R., Snow, C.D.
• Funding Organization(s): National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Stabilizing DNA-Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA

Ward, A.R., Dmytriw, S., Vajapayajula, A., Snow, C.D.

(2022) Crystals (Basel) 12

• DOI: https://doi.org/10.3390/cryst12010049

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.95 kDa 
• Atom Count: 2,970 
• Modeled Residue Count: 272 
• Deposited Residue Count: 314 
• Unique protein chains: 3
• 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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
UNK-UNK-UNK	D	3	Escherichia coli K-12	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
UNK-UNK-UNK-UNK	E	4	Escherichia coli K-12	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*T)-3')	A	22	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*T)-3')	B	22	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	G [auth C], H [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.578	α = 90
b = 80.715	β = 122.63
c = 73.299	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: 2021-09-01 
Deposition Author(s): Ward, A.R., Snow, C.D.

---

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

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2022-03-09
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description