3C28 | pdb_00003c28

Crystal structure of the product synapse complex

PDB DOI: https://doi.org/10.2210/pdb3C28/pdb
NAKB: 3C28

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.292 (Depositor), 0.304 (DCC)
R-Value Work:
0.225 (Depositor)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Detailed study on Synapsis in Cre-loxP recombination reaction

Ghosh, K., Van Duyne, G.D.

To be published.

Macromolecule Content

Total Structure Weight: 93.72 kDa
Atom Count: 6,602
Modeled Residue Count: 682
Deposited Residue Count: 712
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombinase cre	C [auth A], D [auth B]	322	N/A	Mutation(s): 0 Gene Names: cre
UniProt
Find proteins for P06956 (Escherichia phage P1) Explore P06956 Go to UniProtKB: P06956
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06956
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
LoxP DNA, chain C	A [auth C]	34	N/A
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
LoxP DNA, chain D	B [auth D]	34	N/A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.292 (Depositor), 0.304 (DCC)
R-Value Work: 0.225 (Depositor)
R-Value Observed: 0.228 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.254	α = 90
b = 122.453	β = 90
c = 178.991	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-02-17

Deposition Author(s):

Van Duyne, G.D.

Revision History (Full details and data files)

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, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.