3RMP | pdb_00003rmp

Structural basis for the recognition of attP substrates by P4-like integrases

• PDB DOI: https://doi.org/10.2210/pdb3RMP/pdb
• NAKB: 3RMP

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-04-21 Released: 2012-04-25 
• Deposition Author(s): Szwagierczak, A., Popowicz, G.M., Holak, T.A., Rakin, A., Antonenka, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.280 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the recognition of attP substrates by P4-like integrases

Szwagierczak, A., Popowicz, G.M., Holak, T.A., Rakin, A., Antonenka, U.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.56 kDa 
• Atom Count: 2,348 
• Modeled Residue Count: 207 
• Deposited Residue Count: 236 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CP4-like integrase	A, B [auth C]	88	Yersinia pestis	Mutation(s): 0  Gene Names: int, int2, YPO1917, YP_1660, y2393
UniProt
Find proteins for Q9Z3B4 (Yersinia pestis) Explore Q9Z3B4  Go to UniProtKB:  Q9Z3B4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*AP*AP*TP*GP*AP*CP*CP*AP*CP*CP*AP*AP*TP*A)-3'	C [auth E], E [auth G]	15	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*TP*AP*TP*TP*GP*GP*TP*GP*GP*TP*CP*AP*TP*TP*A)-3'	D [auth F], F [auth H]	15	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.280 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.9	α = 90
b = 69.49	β = 90
c = 83.74	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Szwagierczak, A., Popowicz, G.M., Holak, T.A., Rakin, A., Antonenka, U.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description