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- PDB-2elg: The rare crystallographic structure of d(CGCGCG)2: The natural sp... -

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Basic information

Entry
Database: PDB / ID: 2elg
TitleThe rare crystallographic structure of d(CGCGCG)2: The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)2 at 10 degree celsius
ComponentsDNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3')
KeywordsDNA / d(CGCGCG)2 / left-handed Z-DNA / spermidine / polyamine
Function / homologySPERMIDINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsOhishi, H. / Tozuka, Y. / Zhou, D.Y. / Ishida, T. / Nakatani, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: The rare crystallographic structure of d(CGCGCG)(2): The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)(2) at 10 degrees C
Authors: Ohishi, H. / Tozuka, Y. / Da-Yang, Z. / Ishida, T. / Nakatani, K.
History
DepositionMar 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3')
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8627
Polymers3,6202
Non-polymers2415
Water1,20767
1
A: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3')
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3')
hetero molecules

A: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3')
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,72314
Polymers7,2414
Non-polymers48210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-22.2 kcal/mol
Surface area2590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.847, 30.988, 44.022
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3')


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.681153 Å3/Da / Density % sol: 26.83592 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10mM Sodium cacodilate, 1M Magnesium chloride, 100mM spermidine trichloride, 8%MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium cacodilate11
2Magnesium chloride11
3spermidine trichloride11
4MPD11
5HOH11
6Sodium cacodilate12
7Magnesium chloride12
8MPD12
9HOH12

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→25 Å / Num. obs: 11287 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 5.3 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.057 / Net I/σ(I): 20.7
Reflection shellHighest resolution: 1 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.047 / Mean I/σ(I) obs: 20.7 / Num. unique all: 11287 / Rsym value: 0.057 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MERLOTphasing
X-PLOR3.851refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DJ6

1dj6


Resolution: 1→7 Å / Isotropic thermal model: Isotropic / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 520 -random
Rwork0.232 ---
all0.253 11287 --
obs0.244 11232 99.5 %-
Displacement parametersBiso mean: 5.8 Å2
Refinement stepCycle: LAST / Resolution: 1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 273 36 201 510

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