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- PDB-1ehv: A NEW CRYSTAL STRUCTURE FOR THE DODECAMER C-G-C-G-A-A-T-T-C-G-C-G... -

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Basic information

Entry
Database: PDB / ID: 1ehv
TitleA NEW CRYSTAL STRUCTURE FOR THE DODECAMER C-G-C-G-A-A-T-T-C-G-C-G: SYMMETRY EFFECTS ON SEQUENCE-DEPENDENT DNA STRUCTURE
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / DICKERSON DODECAMER / CRYSTAL PACKING
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsJohansson, E.M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: A new crystal form for the dodecamer C-G-C-G-A-A-T-T-C-G-C-G: symmetry effects on sequence-dependent DNA structure.
Authors: Johansson, E. / Parkinson, G. / Neidle, S.
History
DepositionFeb 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6631
Polymers3,6631
Non-polymers00
Water86548
1
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+2/31
Unit cell
Length a, b, c (Å)26.390, 26.390, 98.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Cell settingtrigonal
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-26-

HOH

21A-39-

HOH

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Components

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


Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: KCL, BACL2, MPD, SPERMINE TETRAHYDROCHLORIDE, SODIUM CACODYLATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCL11
2BACL211
3SODIUM CACODYLATE11
4SPERMINE TETRAHYDROCHLORIDE11
5MPD11
6MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mMDNA1drop
2sodium cacodylate1drop
32 mMminor-groove binding drug1drop
410 %MPD1drop
512 mMspermine tetrahydrochloride1drop
680 mM1dropKCl
720 mM1dropBaCl2
830 %MPD1reservoir

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Data collection

DiffractionMean temperature: 284 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 3916 / Num. obs: 2685 / % possible obs: 68.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.206 / % possible all: 0.62

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.312 316 10.5 %RANDOM
Rwork0.238 ---
all0.2455 2997 --
obs0.224 2997 84.43 %-
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 243 0 48 291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.017
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.006
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.007
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
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: 0.301
Solvent computation
*PLUS
Displacement parameters
*PLUS

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