8CRY | pdb_00008cry

Crystal structure of alien DNA CTSZZPBSBSZPPBAG in an orthorhombic lattice

PDB DOI: https://doi.org/10.2210/pdb8CRY/pdb
NAKB: 8CRY

Classification: DNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2022-05-12 Released: 2023-05-17
Deposition Author(s): Georgiadis, M.M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.237 (Depositor), 0.250 (DCC)
R-Value Work:
0.214 (Depositor), 0.220 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Alien DNA visualized at high resolution in A- and B-forms

Georgiadis, M.M., Hoshika, S., Shukla, M., Benner, S.A.

To be published.

Macromolecule Content

Total Structure Weight: 10.19 kDa
Atom Count: 840
Modeled Residue Count: 32
Deposited Residue Count: 32
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPTP(JSP)P(1W5)P(1W5)P(1WA)P(IGU)P(JSP)P(IGU)P(JSP)P(1W5)P(1WA)P(1WA)P(IGU)PAPG)-3')	A, B	16	synthetic construct
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 C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.20 Å
R-Value Free: 0.237 (Depositor), 0.250 (DCC)
R-Value Work: 0.214 (Depositor), 0.220 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.052	α = 90
b = 45.799	β = 90
c = 50.55	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-17

Deposition Author(s):

Georgiadis, M.M.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	193908

Revision History (Full details and data files)

Version 1.0: 2023-05-17
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection

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.