7BPG | pdb_00007bpg

Structure of serinol nucleic acid - RNA complex

PDB DOI: https://doi.org/10.2210/pdb7BPG/pdb
NAKB: 7BPG

Classification: RNA/NUCLEIC ACID
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2020-03-22 Released: 2020-11-25
Deposition Author(s): Kamiya, Y., Satoh, T., Kodama, A., Suzuki, T., Uchiyama, S., Kato, K., Asanuma, H.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.271 (Depositor), 0.271 (DCC)
R-Value Work:
0.232 (Depositor), 0.233 (DCC)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7BPG

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

Literature

Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA

Kamiya, Y., Satoh, T., Kodama, A., Suzuki, T., Murayama, K., Kashida, H., Uchiyama, S., Kato, K., Asanuma, H.

(2020) Commun Chem

DOI: https://doi.org/10.1038/s42004-020-00400-2

Macromolecule Content

Total Structure Weight: 20.34 kDa
Atom Count: 1,395
Modeled Residue Count: 63
Deposited Residue Count: 64
Unique nucleic acid chains: 2

Macromolecules

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA (5'-R(GPCPUPGPCP(5BU)PGPC)-3')	A, B [auth C], C [auth E], D [auth G]	8	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)	E [auth B], F [auth D], G [auth F], H	8	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.271 (Depositor), 0.271 (DCC)
R-Value Work: 0.232 (Depositor), 0.233 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.363	α = 90
b = 46.918	β = 114.54
c = 47.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-11-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2020-11-25
Type: Initial release
Version 1.1: 2024-03-27
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.