3C29 | pdb_00003c29

Cre-loxP Synaptic structure

• PDB DOI: https://doi.org/10.2210/pdb3C29/pdb
• NAKB: 3C29

• Classification: recombination/DNA
• Organism(s): Escherichia phage P1
• Mutation(s): No 


• Deposited: 2008-01-24 Released: 2009-02-17 
• Deposition Author(s): Ghosh, K., Van Duyne, G.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Synapsis study in detail

Ghosh, K., Van Duyne, G.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 187.78 kDa 
• Atom Count: 13,461 
• Modelled Residue Count: 1,425 
• Deposited Residue Count: 1,425 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombinase cre	A, B, E [auth G], F [auth H]	322	N/A	Mutation(s): 0  Gene Names: cre
UniProt
Find proteins for P06956 (Escherichia phage P1) Explore P06956  Go to UniProtKB:  P06956

Entity ID: 2
Molecule	Chains	Length	Organism	Image
LoxP DNA, chain C,	C	35	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
LoxP DNA, chain D,F	D, H [auth F]	34	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
LoxP DNA, chain E	G [auth E]	34	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.413	α = 90
b = 136.413	β = 90
c = 218.826	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Ghosh, K., Van Duyne, G.D.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description