5CY1 | pdb_00005cy1

Tn3 resolvase - site III complex crystal form I

PDB DOI: https://doi.org/10.2210/pdb5CY1/pdb
NAKB: 5CY1

Classification: HYDROLASE, LIGASE/DNA
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-07-30 Released: 2017-01-11
Deposition Author(s): Montano, S.P., Rice, P.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.292 (Depositor), 0.317 (DCC)
R-Value Work:
0.248 (Depositor), 0.255 (DCC)
R-Value Observed:
0.251 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5CY1

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

Literature

Tn3 resolvase - accessory site complexes: DNA geometry dictates complex geometry

Montano, S.P., Rice, P.A.

To be published.

Macromolecule Content

Total Structure Weight: 61.55 kDa
Atom Count: 4,072
Modeled Residue Count: 423
Deposited Residue Count: 444
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transposon Tn3 resolvase	A, B	192	Escherichia coli	Mutation(s): 0 Gene Names: tnpR
UniProt
Find proteins for P0ADI2 (Escherichia coli) Explore P0ADI2 Go to UniProtKB: P0ADI2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ADI2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (30-MER)	C	30	N/A
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA (30-MER)	D	30	N/A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.292 (Depositor), 0.317 (DCC)
R-Value Work: 0.248 (Depositor), 0.255 (DCC)
R-Value Observed: 0.251 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.313	α = 90
b = 77.313	β = 90
c = 272.277	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXDE	phasing
SOLVE	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-01-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM086826

Revision History (Full details and data files)

Version 1.0: 2017-01-11
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2024-03-06
Changes: Data collection, Database references

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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.