PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (2024)

ID or keywords:

Entry

Database: PDB / ID: 1k9l

Title

Solution Structure of DNA TATGAGCGCTCATA

Components

5'-D(*TP*AP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*TP*A)-3'

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (3)

Keywords

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (4)

DNA /

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (5)

Lac operator /

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (6)

double-helix /

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (7)

mutant

Function / hom*ology

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (8)

DNA / DNA (> 10)

Function and hom*ology information

Method

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (10)

SOLUTION NMR /

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (11)

simulated annealing,

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (12)

molecular dynamics, matrix relaxation

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (13)

Authors

Kaluarachchi, K. / Gorenstein, D.G. / Luxon, B.A.

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (14)

Citation

Journal: J.Biomol.Struct.Dyn. / Year: 2000
Title: How Do Proteins Recognize DNA? Solution Structure and Local Conformational Dynamics of Lac Operators by 2D NMR
Authors: Kaluarachchi, K. / Gorenstein, D.G. / Luxon, B.A.

History

Deposition	Oct 29, 2001	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 7, 2001	Provider: repository / Type: Initial release
Revision 1.1	Apr 27, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 23, 2022	Group: Data collection / Database references / Derived calculations Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (17)

Download

PDBx/mmCIF format	1k9l.cif.gz	26.7 KB	Display	PDBx/mmCIF format
PDB format	pdb1k9l.ent.gz	17.5 KB	Display	PDB format
PDBx/mmJSON format	1k9l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k9/1k9l ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k9l	HTTPS FTP

Related structure data

Related structure data	1k9h
Similar structure data	2l2u-d 2hsr-d 1k8l-d 2hpx-d 2esw-d 5ohq-d 1a3m-d 6zyb-d 7jje-d 2yjl-1 Search similar-shape structures by Omokage search (details) F&H Search Similarity search - hom*ologyF&H Search

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (43)

Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#255 - Mar 2021 Cisplatin and DNA similarity (2) #67 - Jul 2005 TATA-Binding Protein similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #23 - Nov 2001 DNA similarity (2) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #135 - Mar 2011 Integrase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (45)

wwPDB /

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (46)

NCBI

Related items in Molecule of the Month

#255 - Mar 2021
Cisplatin and DNA
similarity (2)
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TATA-Binding Protein
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Thymine Dimers
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#168 - Dec 2013
DNA Helicase
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#253 - Jan 2021
Expressome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
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Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
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Transposase
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Catabolite Activator Protein
similarity (1)
#23 - Nov 2001
DNA
similarity (2)
#227 - Nov 2018
Telomerase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: 5'-D(*TP*AP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*TP*A)-3'

B: 5'-D(*TP*AP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*TP*A)-3'

8.56 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

	Theoretical mass	Number of molelcules
Total (without water)	8,560	2
Polymers	8,560	2
Non-polymers	0	0
Water	0

Idetical with deposited unit
defined by author

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	1 / 2	back calculated data agree with experimental NOESY spectrum
Representative		closest to the average

#1: DNA chain	5'-D(TPAPTPGPAPGPCPGPCPTPCPAPTPA)-3' Mass: 4279.804 Da / Num. of mol.: 2 / Mutation: G2A/C13T / Source method: obtained synthetically Details: This sequence is a G2A/C13T mutant of the symmetrized wild-type lac operator sequence.

Experiment

Method:

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (91)

SOLUTION NMR

NMR experiment

Conditions-ID	Experiment-ID	Solution-ID	Type
1	1	1	2D NOESY
2	2	1	2D TOCSY

NMR details

Text: This structure was determined using standard 2D hom*onuclear techniques.

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (94)

Sample preparation

Details	Contents: 3 mM oligonucleotide, 55 mM potassium phosphate, 150 mM KCl, 0.1 mM NaN3 Solvent system: 99.96% D2O
Sample conditions	Ionic strength: 150 mM KCl / pH: 7.4 / Pressure: ambient / Temperature: 298 K

NMR measurement

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M

Radiation wavelength

Relative weight: 1

NMR spectrometer

Type	Manufacturer	Model	Field strength (MHz)	Spectrometer-ID
Varian VXRS	Varian	VXRS	500	1
Varian VXRS	Varian	VXRS	600	2

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (96)

Processing

NMR software

Name	Version	Developer	Classification
Amber	Versions 3-5	Kollman, P.	refinement
MORASS	Version 1.0	Meadows, R.P., Post, C.B. and Gorenstein, D.G.	refinement

Refinement

Method:

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (98)

simulated annealing,

PDB-1k9l: Solution Structure of DNA TATGAGCGCTCATA (99)

molecular dynamics, matrix relaxation
Software ordinal: 1

NMR representative

Selection criteria: closest to the average

NMR ensemble

Conformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 2 / Conformers submitted total number: 1

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