1VE8 | pdb_00001ve8

X-Ray analyses of oligonucleotides containing 5-formylcytosine, suggesting a structural reason for codon-anticodon recognition of mitochondrial tRNA-Met; Part 1, d(CGCGAATT(f5C)GCG)

PDB DOI: https://doi.org/10.2210/pdb1VE8/pdb
NAKB: 1VE8

Classification: DNA
Mutation(s): No

Deposited: 2004-03-29 Released: 2005-06-28
Deposition Author(s): Kimura, K., Ono, A., Watanabe, K., Takenaka, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.279 (Depositor)
R-Value Work:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1VE8

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

Literature

X-Ray analyses of oligonucleotides containing 5-formylcytosine, suggest a structural reason for the codon-anticodon recognition of mitochondrial tRNA-Met

Kimura, K., Ono, A., Watanabe, K., Takenaka, A.

To be published.

Macromolecule Content

Total Structure Weight: 7.41 kDa
Atom Count: 593
Modeled Residue Count: 24
Deposited Residue Count: 24
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
5'-D(CPGPCPGPAPAPTPTP(5FC)PGPCPG)-3'	A, B	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.279 (Depositor)
R-Value Work: 0.221 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.1	α = 90
b = 41.6	β = 90
c = 65.5	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
AMoRE	phasing
CNS	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-06-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-06-28
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: 2023-12-27
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.