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- PDB-1cn0: CRYSTAL STRUCTURE OF D(ACCCT) -

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Basic information

Entry
Database: PDB / ID: 1cn0
TitleCRYSTAL STRUCTURE OF D(ACCCT)
ComponentsDNA (5'-D(*AP*CP*CP*CP*T)-3')
KeywordsDNA / TELOMERE / I-MOTIF
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWeil, J. / Min, T. / Cheng, Y. / Wang, S. / Sutherland, C. / Sinha, N. / Kang, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Stabilization of the i-motif by intramolecular adenine-adenine-thymine base triple in the structure of d(ACCCT).
Authors: Weil, J. / Min, T. / Yang, C. / Wang, S. / Sutherland, C. / Sinha, N. / Kang, C.
History
DepositionMay 24, 1999Deposition site: BNL / Processing site: NDB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*CP*CP*T)-3')
B: DNA (5'-D(*AP*CP*CP*CP*T)-3')
C: DNA (5'-D(*AP*CP*CP*CP*T)-3')
D: DNA (5'-D(*AP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)5,7604
Polymers5,7604
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.810, 93.810, 93.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Cell settingcubic
Space group name H-MI23

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Components

#1: DNA chain
DNA (5'-D(*AP*CP*CP*CP*T)-3')


Mass: 1439.988 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: CHEMICAL SYNTHESIS OF SEQUENCE FROM HUMAN TELOMERIC DNA
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 10%(V/V)2-PROPANOL, 20%(V/V)ETHANOL, 1.0M(NH4)2SO4, 1.5M NACL, 5MM MGCL2 AND 2MM SPERMINE., pH 7, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
12-PROPANOL11
2ETHANOL11
3(NH4)2SO411
4NACL11
5MGCL211
6SPERMINE11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMprotein1drop
25 %(v/v)2-propanol1drop
310 %(v/v)ethanol1drop
40.5 Mammonium sulfate1drop
5150 mM1dropNaCl
65 mM1dropMgCl2
72 mMspermine1drop

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Data collection

DiffractionMean temperature: 103.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 7136 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.035 / Rsym value: 3.5
Reflection shellResolution: 2.2→2.3 Å / % possible all: 96.3
Reflection
*PLUS
Rmerge(I) obs: 0.045

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 191D

191d


Resolution: 2.2→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.235 689 10 %RANDOM
Rwork0.192 ---
obs0.192 6914 98.5 %-
Refine analyzeLuzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 360 0 62 422
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.574
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.067
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: DNA-RAN_REF.PARAM / Topol file: DNA-RNA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.192 / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.07
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg0.57

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