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- PDB-1d16: STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WIT... -

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Basic information

Entry
Database: PDB / ID: 1d16
TitleSTRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*GP*TP*TP*TP*TP*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA STEM / SINGLE STRAND / HAIRPIN LOOP
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsChattopadhyaya, R. / Grzeskowiak, K. / Dickerson, R.E.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Structure of a T4 hairpin loop on a Z-DNA stem and comparison with A-RNA and B-DNA loops.
Authors: Chattopadhyaya, R. / Grzeskowiak, K. / Dickerson, R.E.
#1: Journal: Nature / Year: 1988
Title: X-Ray Structure of a DNA Hairpin Molecule
Authors: Chattopadhyaya, R. / Ikuta, S. / Grzeskowiak, K. / Dickerson., R.E.
History
DepositionApr 12, 1988Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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*GP*CP*GP*CP*GP*TP*TP*TP*TP*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,8821
Polymers4,8821
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.180, 21.630, 36.400
Angle α, β, γ (deg.)90.00, 95.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 4882.139 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density meas: 1.5 Mg/m3 / Density % sol: 44.32 %
Crystal growTemperature: 280 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 280.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2ISOPROPANOL11
3NA CACODYLATE11
4SPERMINE_HCL11
5SR NITRATE11
6WATER12
7ISOPROPANOL12
Crystal grow
*PLUS
Temperature: 7 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mMsodium cacodylate1drop
220 mMspermine tetrachloride1drop
35 mMstrontium nitrate1drop
41 mMDNA1drop
540 %isopropanol1reservoir
61
71

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Data collection

DiffractionMean temperature: 278 K
DetectorType: SYNTEX P1 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 2825
Reflection
*PLUS
Highest resolution: 2.1 Å

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 2.1 Å / σ(F): 2 /
RfactorNum. reflection
obs0.2 1509
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 323 0 70 393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.016
X-RAY DIFFRACTIONn_angle_d0.043
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.1 Å / σ(F): 2 / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.016
X-RAY DIFFRACTIONn_angle_d0.043

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