3T8P | pdb_00003t8p

Crystal structure of d(CGGGTACCCG)4 as a four-way Holliday junction

PDB DOI: https://doi.org/10.2210/pdb3T8P/pdb
NAKB: 3T8P

Classification: DNA
Mutation(s): No

Deposited: 2011-08-01 Released: 2011-12-21
Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.278 (Depositor), 0.278 (DCC)
R-Value Work:
0.235 (Depositor), 0.232 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure of d(CGGGTACCCG)(4) as a four-way Holliday junction

Mandal, P.K., Venkadesh, S., Gautham, N.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1506-1510

PubMed: 22139153 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309111046616
Primary Citation Related Structures:
3T8P

PubMed Abstract:
The crystal structure of the decamer sequence d(CGGGTACCCG)(4) as a four-way Holliday junction has been determined at 2.35 Å resolution. The sequence was designed in order to understand the principles that govern the relationship between sequence and branching structure. It crystallized as a four-way junction structure with an overall geometry similar to those of previously determined Holliday junction structures.

Organizational Affiliation

CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, India.

Macromolecule Content

Total Structure Weight: 6.13 kDa
Atom Count: 423
Modeled Residue Count: 20
Deposited Residue Count: 20
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(CPGPGPGPTPAPCPCPCPG)-3')	A, B	10	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.278 (Depositor), 0.278 (DCC)
R-Value Work: 0.235 (Depositor), 0.232 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.289	α = 90
b = 23.597	β = 111.3
c = 37.124	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-12-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-12-21
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, 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.