7U8B | pdb_00007u8b

Product of 14mer primer with activated asymmetric GA dimer diastereomer 1

PDB DOI: https://doi.org/10.2210/pdb7U8B/pdb
NAKB: 7U8B

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

Deposited: 2022-03-08 Released: 2023-03-15
Deposition Author(s): Fang, Z., Szostak, J.W.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.247 (Depositor), 0.268 (DCC)
R-Value Work:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7U8B

Ligand Structure Quality Assessment

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

Literature

Understanding the metal ion function in the RNA non-enzymatic extesion with phosphorothioates

Pazienza, L.T., Fang, Z., Szostak, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 10.35 kDa
Atom Count: 764
Modeled Residue Count: 30
Deposited Residue Count: 30
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA (5'-R((TLN)P(LCC)P(LCC)P(LCG)PAPCPUPUPAPAPGPUPCPGP*(G46))-3')	A, B	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LXR Query on LXR 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]	5'-O-[(S)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]adenosine C₁₃ H₁₇ N₈ O₆ P VRUNWCWGNRYOCC-WOUKDFQISA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.247 (Depositor), 0.268 (DCC)
R-Value Work: 0.194 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.455	α = 90
b = 43.455	β = 90
c = 81.122	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE 1607034
National Science Foundation (NSF, United States)	United States	CHE 2104708

Revision History (Full details and data files)

Version 1.0: 2023-03-15
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description

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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.