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- PDB-376d: A ZIPPER-LIKE DNA DUPLEX D(GCGAAAGCT) -

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Basic information

Entry
Database: PDB / ID: 376d
TitleA ZIPPER-LIKE DNA DUPLEX D(GCGAAAGCT)
ComponentsDNA (5'-D(*GP*(CBR)P*GP*AP*AP*AP*GP*CP*T)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / OVERHANGING BASE / MODIFIED / MISMATCHED
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD AT BROMINE EDGE / Resolution: 2.1 Å
AuthorsCruse, W.B.T. / Shepard, W. / Prange, T. / delalFortelle, E. / Fourme, R.
Citation
Journal: Structure / Year: 1998
Title: A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.
Authors: Shepard, W. / Cruse, W.B. / Fourme, R. / de la Fortelle, E. / Prange, T.
#1: Journal: Science / Year: 1997
Title: RNA Tertiary Structure Mediation by Adenosine Platforms
Authors: Cate, J.H. / Gooding, A.R. / Podell, E. / Zhou, K. / Golden, B.L. / Szewczak, A.A. / Kundrot, C.E. / Cech, T.R. / Doudna, J.A.
#2: Journal: Structure / Year: 1997
Title: Solution Structure of a Metal-binding Site in the Major Groove of RNA Complexed with Cobalt(III) Hexammine
Authors: Kieft, J.S. / Tinoco Jr., I.
#3: Journal: Nucleic Acids Res. / Year: 1989
Title: Extraordinary Stable Structure of Short Single-Stranded DNA Fragments Containing a Specific Base Sequence: d(GCGAAAGC)
Authors: Hirao, I. / Nichimura, Y. / Naraoka, T. / Watanabe, K. / Arata, Y. / Miura, K.
#4: Journal: Biochemistry / Year: 1985
Title: Structural Basis for Stabilisation of Z-DNA by Cobalt Haxaammine and Magnesium Cations
Authors: Geissner, R.V. / Quigley, G.J. / Wang, H.J. / van der Marel, A. / van Boom, J.H.
History
DepositionJan 22, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 26, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*(CBR)P*GP*AP*AP*AP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0052
Polymers2,8441
Non-polymers1611
Water32418
1
A: DNA (5'-D(*GP*(CBR)P*GP*AP*AP*AP*GP*CP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*(CBR)P*GP*AP*AP*AP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0104
Polymers5,6872
Non-polymers3222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)37.560, 37.560, 65.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Cell settinghexagonal
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-10-

NCO

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Components

#1: DNA chain DNA (5'-D(*GP*(CBR)P*GP*AP*AP*AP*GP*CP*T)-3')


Mass: 2843.733 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 36 %
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2CACODYLATECacodylic acid11
3[CO(NH3)6]3+11
4MPD11
Crystal
*PLUS
Density % sol: 36 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
20.05 Mlithium cacodylate1drop0.4ml
30.1 M1drop0.003mlNH4OH
410 mMcobalt hexammine chloride1drop0.015ml
550 %MPD1drop0.008ml
625 %MPD1reservoir
1protein1drop1mg

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Data collection

DiffractionMean temperature: 276 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW21B
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: DOUBLE MONO + MULTILAYER FOCUS
RadiationMonochromator: SI(III) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 1832 / % possible obs: 95 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.3
Reflection shellHighest resolution: 2.1 Å / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 4.2 / % possible all: 61
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 15 Å / % possible obs: 95 % / Observed criterion σ(I): 3 / Redundancy: 11.6 % / Num. measured all: 21345
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
MADLSQ+ CCP4 PACKAGEmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MADLSQphasing
CCP4phasing
RefinementMethod to determine structure: MAD AT BROMINE EDGE
Starting model: MANUALLY BUILT IN THE EXPERIMENTAL DENSITY

Resolution: 2.1→15 Å
RfactorNum. reflection% reflection
Rfree0.241 183 10 %
Rwork0.189 --
obs0.189 1832 95 %
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 15 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 184 4 18 206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d0.023
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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