2DPU | pdb_00002dpu

Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA

• PDB DOI: https://doi.org/10.2210/pdb2DPU/pdb
• NAKB: 2DPU

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-15 Released: 2007-05-15 
• Deposition Author(s): Vivian, J.P., Wilce, J., Wilce, M.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.306 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA

Vivian, J.P., Wilce, J., Wilce, M.C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.92 kDa 
• Atom Count: 1,396 
• Modeled Residue Count: 136 
• Deposited Residue Count: 143 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication termination protein	C [auth A]	122	Bacillus subtilis	Mutation(s): 1  Gene Names: rtp
UniProt
Find proteins for P0CI76 (Bacillus subtilis (strain 168)) Explore P0CI76  Go to UniProtKB:  P0CI76

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(P*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'	A [auth D]	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*T)-3'	B [auth E]	11	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.306 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.049	α = 90
b = 73.049	β = 90
c = 68.411	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Vivian, J.P., Wilce, J., Wilce, M.C.J.

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references
• Version 1.5: 2024-05-29
  Changes: Data collection