3G2R | pdb_00003g2r

Crystal structure of d(CACGCG).d(CGCGTG) cocrystallized with MnCl2

PDB DOI: https://doi.org/10.2210/pdb3G2R/pdb
NAKB: 3G2R

Classification: DNA
Mutation(s): No

Deposited: 2009-02-01 Released: 2009-03-03
Deposition Author(s): Venkadesh, S., Mandal, P.K., Kannan, R., Gautham, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.270 (Depositor), 0.344 (DCC)
R-Value Work:
0.269 (Depositor), 0.272 (DCC)
R-Value Observed:
0.269 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3G2R

This is version 1.2 of the entry. See complete history.

Literature

Crystal studies of d(CACGCG).d(CGCGTG) grown with various counter ions

Venkadesh, S., Mandal, P.K., Kannan, R., Gautham, N.

To be published.

Macromolecule Content

Total Structure Weight: 2.19 kDa
Atom Count: 131
Modeled Residue Count: 6
Deposited Residue Count: 6
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
5'-D(CPGPTPGPCPG)-3'	A	6	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCM Query on DCM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₇ P NCMVOABPESMRCP-SHYZEUOFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MN Query on MN 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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.270 (Depositor), 0.344 (DCC)
R-Value Work: 0.269 (Depositor), 0.272 (DCC)
R-Value Observed: 0.269 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.878	α = 90
b = 30.97	β = 90
c = 43.405	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-03-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.