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- PDB-362d: THE STRUCTURE OF D(TGCGCA)2 AND A COMPARISON TO OTHER Z-DNA HEXAMERS -

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Basic information

Entry
Database: PDB / ID: 362d
TitleTHE STRUCTURE OF D(TGCGCA)2 AND A COMPARISON TO OTHER Z-DNA HEXAMERS
ComponentsDNA (5'-D(*TP*GP*CP*GP*CP*A)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHarper, N.A. / Brannigan, J.A. / Buck, M. / Lewis, R.J. / Moore, M.H. / Schneider, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of d(TGCGCA)2 and a comparison to other DNA hexamers.
Authors: Harper, A. / Brannigan, J.A. / Buck, M. / Hewitt, L. / Lewis, R.J. / Moore, M.H. / Schneider, B.
History
DepositionAug 20, 1997Deposition site: NDB / Processing site: NDB
SupersessionNov 18, 1997ID: 347D
Revision 1.0Nov 20, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*GP*CP*GP*CP*A)-3')
B: DNA (5'-D(*TP*GP*CP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9414
Polymers3,6182
Non-polymers3222
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.162, 28.670, 44.335
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(*TP*GP*CP*GP*CP*A)-3')


Mass: 1809.218 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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 Å3/Da / Density % sol: 38 %
Crystal growpH: 6 / Details: pH 6.00
Crystal
*PLUS
Density % sol: 38 %
Crystal grow
*PLUS
Temperature: 291 K / pH: 6 / Method: vapor diffusion, sitting drop
Details: drops of 6 micro litter total volume obtained by combining 3 micro litter of stock solution with 3 micro litter of mother liquor
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mMsingle-stranded hexamer1drop
250 mMsodium cacodylate1reservoir
31 mMcobalt hexammine1reservoir
45 mMargininamide chloride1reservoir
530 %(v/v)MPD1reservoir
65 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.3→24 Å / Num. obs: 7024 / % possible obs: 99.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 23.6 / % possible all: 87.4
Reflection shell
*PLUS
% possible obs: 87.4 %

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Processing

Software
NameClassification
AMoREphasing
SHELXL-96refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODIFIED NDB ENTRY ZDF002 (PDB ENTRY 1DCG)

1dcg


Resolution: 1.3→10 Å / Num. parameters: 3018 / Num. restraintsaints: 2782 / σ(F): 0
Details: RESTRAINED ANISOTROPIC REFINEMENT OF NON-HYDROGEN ATOMS. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 1.4%.
RfactorNum. reflection% reflection
Rfree0.173 7005 10 %
all0.12 7005 -
obs0.117 7005 -
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRanisotropic
ALL WATERSX-RAY DIFFRACTIONTRanisotropic
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 138 / Occupancy sum non hydrogen: 332
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 243 14 78 335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.022
X-RAY DIFFRACTIONs_approx_iso_adps0.065
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.12
Solvent computation
*PLUS
Displacement parameters
*PLUS

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