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- PDB-279d: CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAM... -

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Basic information

Entry
Database: PDB / ID: 279d
TitleCRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCGCGCGCGC) IN THE Z-DNA CONFORMATION-PART I
ComponentsDNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3'
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBan, C. / Ramakrishnan, B. / Sundaralingam, M.
CitationJournal: Biophys.J. / Year: 1996
Title: Crystal structure of the self-complementary 5'-purine start decamer d(GCGCGCGCGC) in the Z-DNA conformation. I.
Authors: Ban, C. / Ramakrishnan, B. / Sundaralingam, M.
History
DepositionMay 21, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 27, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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: DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5731
Polymers5731
Non-polymers00
Water25214
1
A: DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3'
x 12


Theoretical massNumber of molelcules
Total (without water)6,88112
Polymers6,88112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-y,x-y,z-1/31
crystal symmetry operation3_555-x+y,-x,z+1/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation6_554x-y,x,z-1/61
crystal symmetry operation7_557y,x,-z+8/31
crystal symmetry operation8_557x-y,-y,-z+21
crystal symmetry operation9_557-x,-x+y,-z+7/31
crystal symmetry operation10_557-y,-x,-z+13/61
crystal symmetry operation11_557-x+y,y,-z+5/21
crystal symmetry operation12_557x,x-y,-z+17/61
Unit cell
Length a, b, c (Å)18.100, 18.100, 43.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-5-

HOH

21A-10-

HOH

31A-12-

HOH

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Components

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


Mass: 573.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 1.78 Å3/Da / Density % sol: 30.78 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMdecamer1drop
220 mMsodium cacodylate1drop
35 mMmagnesium chloride1drop
40.5 mMspermine tetrachloride1drop
55 %(v/v)MPD1drop
645 %MPD1reservoir
71

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR / Date: Apr 13, 1994
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 2020 / Num. obs: 401 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.022
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Redundancy: 5 % / Num. measured all: 2020

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Processing

Software
NameVersionClassification
X-PLORrefinement
XENGENV. 2.0data reduction
RefinementResolution: 1.9→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.186 -
obs0.186 340
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTFisotropic
ALL WATERSX-RAY DIFFRACTIONTFisotropic
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 41 0 14 55
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_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d31
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d3.4
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
Xplor fileSerial no: 1 / Param file: PARAM11.DAT
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg31
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg3.4

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