7OA5 | pdb_00007oa5

RUVA COMPLEXED TO A HOLLIDAY JUNCTION.

• PDB DOI: https://doi.org/10.2210/pdb7OA5/pdb
• Entry: 7OA5 supersedes: 1BVS
• NAKB: 7OA5

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium leprae TN, Mycobacterium leprae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-04-19 Released: 2021-04-28 
• Deposition Author(s): Roe, S.M., Pearl, L.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.250 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1bvs

Literature

Crystal structure of an octameric RuvA-Holliday junction complex

Roe, S.M., Pearl, L.H.

(1998) Molecular Cell 2: 361-372

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 184.62 kDa 
• Atom Count: 11,940 
• Modeled Residue Count: 1,522 
• Deposited Residue Count: 1,684 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Holliday junction ATP-dependent DNA helicase RuvA	A, B, C, D, E, F, G, H	203	Mycobacterium leprae TN	Mutation(s): 0  Gene Names: ruvA, ML0482, B1177_C2_188 EC: 3.6.4.12
UniProt
Find proteins for P40832 (Mycobacterium leprae (strain TN)) Explore P40832  Go to UniProtKB:  P40832

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*TP*CP*GP*CP*GP*AP*GP*TP*TP*CP*GP*C)-3')	I	15	Mycobacterium leprae

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*AP*AP*CP*TP*CP*GP*CP*GP*AP*AP*C)-3')	J	14	Mycobacterium leprae

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*AP*CP*T)-3')	K	16	Mycobacterium leprae

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*AP*CP*T)-3')	L	15	Mycobacterium leprae

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.250 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.35	α = 90
b = 141.35	β = 90
c = 106.47	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Roe, S.M., Pearl, L.H.
• This entry supersedes: 1BVS

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Advisory, Structure summary