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- PDB-1xam: Cobalt hexammine induced tautameric shift in Z-DNA: structure of ... -

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Basic information

Entry
Database: PDB / ID: 1xam
TitleCobalt hexammine induced tautameric shift in Z-DNA: structure of d(CGCGCA).d(TGCGCG) in two crystal forms.
Components
  • CGCGCA
  • TG
  • TGCGCG
KeywordsDNA / DOUBLE HELIX / Z-DNA
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsThiyagarajan, S. / Rajan, S.S. / Gautham, N.
Citation
Journal: Nucleic Acids Res. / Year: 2004
Title: Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms.
Authors: Thiyagarajan, S. / Rajan, S.S. / Gautham, N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of d(TGCGCG). d(CGCGCA) in two crystal forms: effects of sequence and crystal packing in Z-DNA
Authors: Thiyagarajan, S. / Rajan, S.S. / Gautham, N.
History
DepositionAug 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.5Apr 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: CGCGCA
B: TGCGCG
D: TG
E: TG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9575
Polymers4,7964
Non-polymers1611
Water32418
1
A: CGCGCA
B: TGCGCG


Theoretical massNumber of molelcules
Total (without water)3,6192
Polymers3,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: TG
E: TG
hetero molecules

D: TG
E: TG
hetero molecules

D: TG
E: TG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0149
Polymers3,5316
Non-polymers4833
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x-y,x-1,z-1/61
crystal symmetry operation5_665y+1,-x+y+1,z+1/61
Unit cell
Length a, b, c (Å)35.588, 35.588, 44.518
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Detailsbiological unit is a double helix. A second hexamer is to be generated by symmetry related entities of the dinucleotide formed with chain C and D.

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Components

#1: DNA chain CGCGCA


Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain TGCGCG


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain TG


Mass: 588.441 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#5: 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: 1

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Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 29.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: MPD, cacodylate, cobalt hexammine chloride, spermine., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2cacodylateCacodylic acid11
3cobalt hexammine chloride11
4spermine11
5H2O11
6MPD12
7cacodylateCacodylic acid12
8H2O12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 25, 2004
RadiationMonochromator: NIL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. all: 2695 / Num. obs: 2686 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.64 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 2.4
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 4.34 % / Rmerge(I) obs: 0.5274 / Mean I/σ(I) obs: 1 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
AUTOMARdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Z-DNA hexamer with terminal base pairs replaced with A-T base pair.

Resolution: 1.86→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.879 / SU B: 7.847 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.294 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.34618 199 7.4 %RANDOM
Rwork0.27283 ---
all0.295 2595 --
obs0.27867 2495 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.86→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 324 7 18 349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0420.021366
X-RAY DIFFRACTIONr_angle_refined_deg7.2353563
X-RAY DIFFRACTIONr_chiral_restr0.3870.249
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.02167
X-RAY DIFFRACTIONr_nbd_refined0.260.3133
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.514
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.470.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4830.53
X-RAY DIFFRACTIONr_scbond_it5.623366
X-RAY DIFFRACTIONr_scangle_it6.8484.5563
LS refinement shellResolution: 1.86→1.909 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.483 12
Rwork0.431 151

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