5K1Y | pdb_00005k1y

P2(1) Structure of pNOB8 AspA-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb5K1Y/pdb
• Entry: 5K1Y supersedes: 4RU7, 5FC0
• NAKB: 5K1Y

• Classification: TRANSCRIPTION/DNA
• Organism(s): Sulfolobus sp. NOB8H2, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-05-18 Released: 2016-06-15 
• Deposition Author(s): Schumacher, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Detailed structural analysis of AspA-DNA contacts

Schumacher, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 83.8 kDa 
• Atom Count: 5,772 
• Modeled Residue Count: 611 
• Deposited Residue Count: 618 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AspA	A [auth C], B [auth D], C [auth A], D [auth B], G [auth E], H [auth F]	92	Sulfolobus sp. NOB8H2	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	E [auth P]	33	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	F [auth N]	33	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.366	α = 90
b = 72.306	β = 114.72
c = 90.508	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Schumacher, M.
• This entry supersedes: 4RU7, 5FC0

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2016-08-17
  Changes: Other
• Version 1.2: 2019-02-06
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references