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- PDB-260d: CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAM... -

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Basic information

Entry
Database: PDB / ID: 260d
TitleCRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II
ComponentsDNA (5'-D(*GP*CP*AP*CP*GP*CP*GP*TP*GP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBan, C. / Sundaralingam, M.
CitationJournal: Biophys.J. / Year: 1996
Title: Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II.
Authors: Ban, C. / 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*AP*CP*GP*CP*GP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)3,0461
Polymers3,0461
Non-polymers00
Water73941
1
A: DNA (5'-D(*GP*CP*AP*CP*GP*CP*GP*TP*GP*C)-3')

A: DNA (5'-D(*GP*CP*AP*CP*GP*CP*GP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)38.970, 38.970, 77.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-13-

HOH

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Components

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


Mass: 3045.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4[CO(NH3)6]3+11
5WATER12
6MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMDNA dodecamer1drop
240 mMsodium cacodylate1drop
30.5 mMcobalt hexamine1drop
445 %MPD1reservoir
51
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR / Date: Dec 6, 1994
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→8 Å / Num. all: 9346 / Num. obs: 2634 / % possible obs: 91 % / Observed criterion σ(F): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.031
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / % possible obs: 91 % / Observed criterion σ(F): 1 / Redundancy: 3.5 % / Num. measured all: 9346

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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 2491
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTFisotropic
ALL WATERSX-RAY DIFFRACTIONTFisotropic
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 0 41 243
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d32.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d3.2
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: PARAM_NDB.DNA
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_deg32.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg3.2

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