2DPD | pdb_00002dpd

Crystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site

• PDB DOI: https://doi.org/10.2210/pdb2DPD/pdb
• NAKB: 2DPD

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-05-09 Released: 2007-05-15 
• Deposition Author(s): Vivian, J.P., Wilce, J., Wilce, M.C.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site

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: 41.94 kDa 
• Atom Count: 2,806 
• Modeled Residue Count: 274 
• Deposited Residue Count: 286 
• 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], D [auth B]	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(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*AP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'	A [auth D]	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*TP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'	B [auth E]	21	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.006	α = 90
b = 117.006	β = 90
c = 165.553	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	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: 2021-11-10
  Changes: Database references
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description