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- PDB-5ana: THE CRYSTAL STRUCTURE OF D(GTACGTAC) AT 2.25 ANGSTROMS RESOLUTION... -

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Basic information

Entry
Database: PDB / ID: 5ana
TitleTHE CRYSTAL STRUCTURE OF D(GTACGTAC) AT 2.25 ANGSTROMS RESOLUTION. ARE THE A-DNA'S ALWAYS UNWOUND APPROXIMATELY 10 DEGREES AT THE C-G STEPS
ComponentsDNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsTakusagawa, F.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 1990
Title: The crystal structure of d(GTACGTAC) at 2.25 A resolution: are the A-DNA's always unwound approximately 10 degrees at the C-G steps
Authors: Takusagawa, F.
History
DepositionOct 31, 1989Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,4512
Polymers2,4271
Non-polymers241
Water93752
1
A: DNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,9024
Polymers4,8532
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)42.320, 42.320, 25.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-ID
220 mMsodium cacodylate1drop
310 mMmagnesium chloride1drop
42 mMspermine tetrachloride1drop
540 %(v/v)MPD1reservoir
1mMDNA1drop

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Data collection

DiffractionMean temperature: 263 K
DetectorDetector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→25 Å / Num. all: 2348 / Num. obs: 1233
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 25 Å

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Processing

SoftwareName: CORELS / Classification: refinement
RefinementResolution: 2.25→25 Å /
RfactorNum. reflection
obs0.184 1233
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
WATER MOLECULESX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 1 52 214
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 25 Å / Num. reflection obs: 1233 / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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