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- PDB-1dc0: CRYSTAL STRUCTURE OF AN A/B-DNA INTERMEDIATE CATGGGCCCATG -

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Basic information

Entry
Database: PDB / ID: 1dc0
TitleCRYSTAL STRUCTURE OF AN A/B-DNA INTERMEDIATE CATGGGCCCATG
ComponentsDNA (5'-D(*CP*AP*TP*GP*GP*GP*CP*CP*CP*AP*TP*G)-3')
KeywordsDNA / A-DNA / B-DNA / INTERMEDIATE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS BASED ON THE IODINATED SEQUENCE D(CAT(IODO-G)GGCCCATG) / Resolution: 1.3 Å
AuthorsNg, H.L. / Kopka, M.L. / Dickerson, R.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The structure of a stable intermediate in the A ;-> B DNA helix transition
Authors: Ng, H.L. / Kopka, M.L. / Dickerson, R.E.
History
DepositionNov 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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(*CP*AP*TP*GP*GP*GP*CP*CP*CP*AP*TP*G)-3')
B: DNA (5'-D(*CP*AP*TP*GP*GP*GP*CP*CP*CP*AP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.197, 40.197, 77.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: DNA chain DNA (5'-D(*CP*AP*TP*GP*GP*GP*CP*CP*CP*AP*TP*G)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.3MM DUPLEX DNA, 120 MM CALCIUM ACETATE, 4.8 MM SPERMINE, 60 MM SODIUM CACODYLATE BUFFER, PH 7.0, 9.5% MPD IN DROP, 25% MPD IN RESERVOIR, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1CALCIUM ACETATE11
2SPERMINE11
3SODIUM CACODYLATE11
4MPD11
5MPD12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.3 mMduplex DNA1drop
2120 mMCa-acetate1drop
34.8 mMspermine1drop
460 mMNa cacodylate1drop
59.5 %(v/v)1drop
625 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 0.978
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. all: 16190 / Num. obs: 16190 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 43.6
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.179 / % possible all: 91.2
Reflection
*PLUS
Num. obs: 16111 / % possible obs: 98.6 % / Num. measured all: 128129 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 7.6

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Processing

Software
NameClassification
DMmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: SIRAS BASED ON THE IODINATED SEQUENCE D(CAT(IODO-G)GGCCCATG)
Resolution: 1.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.19 800 5 %RANDOM
Rwork0.168 ---
all0.172 16111 --
obs0.172 16111 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 93 579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.016
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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