3GJH | pdb_00003gjh

Crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one

PDB DOI: https://doi.org/10.2210/pdb3GJH/pdb
NAKB: 3GJH

Classification: DNA
Mutation(s): No

Deposited: 2009-03-09 Released: 2010-03-31
Deposition Author(s): Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.306 (Depositor), 0.289 (DCC)
R-Value Work:
0.259 (Depositor), 0.266 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one

Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T., Ohkubo, A., Sekine, M., Shibata, T., Millington, C.L.

To be published.

Macromolecule Content

Total Structure Weight: 7.68 kDa
Atom Count: 529
Modeled Residue Count: 24
Deposited Residue Count: 24
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
5'-D(CPGPCPGPAPAPTPTP(B7C)PGPCPG)-3'	A, B	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DAP Query on DAP 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]	6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE C₁₆ H₁₅ N₅ FWBHETKCLVMNFS-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: 2.90 Å
R-Value Free: 0.306 (Depositor), 0.289 (DCC)
R-Value Work: 0.259 (Depositor), 0.266 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.207	α = 90
b = 41.379	β = 90
c = 64.866	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 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.