1ENN | pdb_00001enn

SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE OF D(GCGAATTCG)2 AT ATOMIC RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1ENN/pdb
Entry: 1ENN supersedes: 475D
NAKB: 1ENN

Classification: DNA
Mutation(s): No

Deposited: 2000-03-21 Released: 2000-05-03
Deposition Author(s): Soler-Lopez, M., Malinina, L., Subirana, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.89 Å
R-Value Free:
0.161 (Depositor), 0.150 (DCC)
R-Value Work:
0.135 (Depositor), 0.154 (DCC)
R-Value Observed:
0.135 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Solvent organization in an oligonucleotide crystal. The structure of d(GCGAATTCG)2 at atomic resolution.

Soler-Lopez, M., Malinina, L., Subirana, J.A.

(2000) J Biological Chem 275: 23034-23044

PubMed: 10749874 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M002119200
Primary Citation Related Structures:
1ENN

PubMed Abstract:
We describe the crystal structure of d(GCGAATTCG) determined by x-ray diffraction at atomic resolution level (0.89 A). The duplex structure is practically identical to that described at 2.05 A resolution (Van Meervelt, L., Vlieghe, D., Dautant, A., Gallois, B., Précigoux, G., and Kennard, O. (1995) Nature 374, 742-744), however about half of the phosphate groups show multiple conformations. The crystal has three regions with different solvent structure. One of them contains several ordered Mg(+2) ions and can be considered as an ionic crystal. A second region is formed by a network of ordered water molecules with a polygonal organization that binds three duplexes. The third region is formed by channels of solvent in which very few ordered solvent molecules are visible. The less ordered phosphates are found facing this channel. The latter region provides a view of DNA with highly movable charges, both negative phosphates and counterions, without a precise location.

Organizational Affiliation

Departament d'Enginyeria Quimica, Universitat Politécnica de Catalunya, E-08028 Barcelona, Spain.

Macromolecule Content

Total Structure Weight: 5.77 kDa
Atom Count: 568
Modeled Residue Count: 18
Deposited Residue Count: 18
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(GPCPGPAPAPTPTPCP*G)-3')	A, B	9	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
O Query on O Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A], L [auth B], M [auth B]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.89 Å
R-Value Free: 0.161 (Depositor), 0.150 (DCC)
R-Value Work: 0.135 (Depositor), 0.154 (DCC)
R-Value Observed: 0.135 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 21.938	α = 90
b = 36.54	β = 90
c = 52.728	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
SHELXL-97	refinement
X-PLOR	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2000-05-03

Deposition Author(s):

Soler-Lopez, M.

Malinina, L.

Subirana, J.A.

This entry supersedes: 475D

Revision History (Full details and data files)

Version 1.0: 2000-05-03
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations