3OIE | pdb_00003oie

Crystal structure of the DB1880-D(CGCGAATTCGCG)2 complex

PDB DOI: https://doi.org/10.2210/pdb3OIE/pdb
NAKB: 3OIE

Classification: DNA
Mutation(s): No

Deposited: 2010-08-19 Released: 2011-01-19
Deposition Author(s): Lin, S., Neidle, S., Campbell, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.241 (Depositor), 0.246 (DCC)
R-Value Work:
0.163 (Depositor)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of the DB1880-D(CGCGAATTCGCG)2 complex

Lin, S., Neidle, S., Campbell, N.

To be published.

Macromolecule Content

Total Structure Weight: 8.01 kDa
Atom Count: 672
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(CPGPCPGPAPAPTPTPCPGPCPG)-3'	A, B	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
881 Query on 881 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	N',N''-{furan-2,5-diylbis[3-(piperidin-4-yloxy)benzene-4,1-diyl]}dipyridine-2-carboximidamide C₃₈ H₄₀ N₈ O₃ ZOPMAKJQIUYLIW-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.241 (Depositor), 0.246 (DCC)
R-Value Work: 0.163 (Depositor)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.114	α = 90
b = 38.417	β = 90
c = 66.205	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-01-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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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.