4KWX

Linear structure of the Holliday junction sequence (TCGGCGCCGA)

PDB DOI: https://doi.org/10.2210/pdb4KWX/pdb
NAKB: 4KWX

Classification: DNA
Mutation(s): No

Deposited: 2013-05-24 Released: 2014-11-26
Deposition Author(s): Skamrova, G., Laponogov, I., Campbell, N., Neidle, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.187
R-Value Work: 0.173
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

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

Literature

Linear structure of the Holliday junction sequence (TCGGCGCCGA)

Skamrova, G., Laponogov, I., Campbell, N., Neidle, S.

To be published.

Macromolecule Content

Total Structure Weight: 18.52 kDa
Atom Count: 1,503
Modelled Residue Count: 60
Deposited Residue Count: 60
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth E] SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain P [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain L [auth E] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E] mmCIF format, chain O [auth F] mmCIF format, chain P [auth F]	G [auth A] H [auth A] I [auth B] J [auth D] K [auth D] G [auth A], H [auth A], I [auth B], J [auth D], K [auth D], L [auth E], M [auth E], N [auth E], O [auth F], P [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.187
R-Value Work: 0.173
R-Value Observed: 0.174
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.41	α = 101.28
b = 34.49	β = 103.21
c = 34.69	γ = 103.81

Software Package:

Software Name	Purpose
GDE	data collection
PHASER	phasing
PHENIX	refinement
xia2	data reduction
XDS	data reduction
xia2	data scaling
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations