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- PDB-1m6r: Crystal structure of rGd(CGCGCG) forming hexamer Z-DNA duplex wit... -

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Basic information

Entry
Database: PDB / ID: 1m6r
TitleCrystal structure of rGd(CGCGCG) forming hexamer Z-DNA duplex with 5'-(rG) overhang
Components5'-R(*G)D(*CP*GP*CP*GP*CP*G)-3'
KeywordsDNA / Z-DNA / overhang
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsPan, B. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystal structure of rGd(CGCGCG): a Z-DNA hexamer duplex with a 5'-(rG) overhang.
Authors: Pan, B. / Sundaralingam, M.
History
DepositionJul 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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: 5'-R(*G)D(*CP*GP*CP*GP*CP*G)-3'
B: 5'-R(*G)D(*CP*GP*CP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)4,2792
Polymers4,2792
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.96, 31.47, 44.73
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 2139.411 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2-propanol (at reservoir), Spermine tetrachloride, magnesium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Spermine tetrachloride11
2MgCl211
3cacodylate11
42-propanol12
5MgCl212
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMchimera1dropsingle strand concentration
240 mMsodium cacodylate1droppH6.5
320 mM1dropMgCl2
41 mMspermine tetrachloride1drop
510 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 8, 1997 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→29 Å / Num. obs: 3576 / % possible obs: 87.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.54→1.65 Å / Rmerge(I) obs: 0.195 / % possible all: 79.9
Reflection
*PLUS
Num. measured all: 12118
Reflection shell
*PLUS
% possible obs: 79.9 %

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→8 Å / Isotropic thermal model: isotropic / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.191 352 -random
Rwork0.162 ---
obs-3537 87.8 %-
Refinement stepCycle: LAST / Resolution: 1.54→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 63 303
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.3
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_dihedral_angle_d34.4
X-RAY DIFFRACTIONx_improper_angle_d1.2
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 3536 / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg34.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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