3PBX | pdb_00003pbx

Strontium bound to the sequence d(CCGGCGCCGG)

PDB DOI: https://doi.org/10.2210/pdb3PBX/pdb
NAKB: 3PBX

Classification: DNA
Mutation(s): No

Deposited: 2010-10-21 Released: 2011-02-02
Deposition Author(s): Naseer, A., Cardin, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.327 (Depositor), 0.318 (DCC)
R-Value Work:
0.251 (Depositor), 0.245 (DCC)
R-Value Observed:
0.254 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Strontium bound to the sequence d(CCGGCGCCGG)

Naseer, A., Cardin, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 6.2 kDa
Atom Count: 463
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
DNA	A, B	10	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SR Query on SR 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]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.327 (Depositor), 0.318 (DCC)
R-Value Work: 0.251 (Depositor), 0.245 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.89	α = 90
b = 25.001	β = 110.01
c = 37.044	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-02-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Database references, Refinement description, Structure summary
Version 1.3: 2023-09-06
Changes: 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.