1PWF | pdb_00001pwf

One Sugar Pucker Fits All: Pairing Versatility Despite Conformational Uniformity in TNA

PDB DOI: https://doi.org/10.2210/pdb1PWF/pdb
NAKB: 1PWF

Classification: DNA
Mutation(s): No

Deposited: 2003-07-01 Released: 2004-07-13
Deposition Author(s): Pallan, P.S., Wilds, C.J., Wawrzak, Z., Krishnamurthy, R., Eschenmoser, A., Egli, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free:
0.188 (Depositor), 0.172 (DCC)
R-Value Work:
0.133 (Depositor), 0.135 (DCC)
R-Value Observed:
0.133 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Why does TNA cross-pair more strongly with RNA than with DNA? an answer from X-ray analysis.

Pallan, P.S., Wilds, C.J., Wawrzak, Z., Krishnamurthy, R., Eschenmoser, A., Egli, M.

(2003) Angew Chem Int Ed Engl 42: 5893-5895

PubMed: 14673929 Search on PubMed
DOI: https://doi.org/10.1002/anie.200352553
Primary Citation Related Structures:
1PWF

Organizational Affiliation

Department of Biochemistry, Vanderbilt University, Nashville, TN 37332, USA.

Macromolecule Content

Total Structure Weight: 6.32 kDa
Atom Count: 529
Modeled Residue Count: 20
Deposited Residue Count: 20
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
5'-D(GPCPGPTPAP(2MU)P(FA2)PCPGPC)-3'	A, B	10	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPM Query on SPM 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]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-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: 1.16 Å
R-Value Free: 0.188 (Depositor), 0.172 (DCC)
R-Value Work: 0.133 (Depositor), 0.135 (DCC)
R-Value Observed: 0.133 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.429	α = 90
b = 44.522	β = 90
c = 47.332	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
XDS	data scaling
XDS	data reduction
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-07-13

Deposition Author(s):

Krishnamurthy, R.

Eschenmoser, A.

Revision History (Full details and data files)

Version 1.0: 2004-07-13
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Advisory, Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.5: 2023-08-16
Changes: Advisory, Data collection, Database references, Derived calculations, 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.