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- PDB-348d: X-RAY CRYSTAL STRUCTURES OF THE DECAMER DGACCGCGGTC: LOW SALT CON... -

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Basic information

Entry
Database: PDB / ID: 348d
TitleX-RAY CRYSTAL STRUCTURES OF THE DECAMER DGACCGCGGTC: LOW SALT CONCENTRATION
ComponentsDNA (5'-D(*GP*AP*CP*CP*GP*CP*GP*GP*TP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsLuo, M. / Finley, J.B.
CitationJournal: Nucleic Acids Res. / Year: 1998
Title: X-ray crystal structures of half the human papilloma virus E2 binding site: d(GACCGCGGTC).
Authors: Finley, J.B. / Luo, M.
History
DepositionAug 29, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 9, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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*AP*CP*CP*GP*CP*GP*GP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)3,0461
Polymers3,0461
Non-polymers00
Water93752
1
A: DNA (5'-D(*GP*AP*CP*CP*GP*CP*GP*GP*TP*C)-3')

A: DNA (5'-D(*GP*AP*CP*CP*GP*CP*GP*GP*TP*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_655-x+y+1,y,-z+1/21
Unit cell
Length a, b, c (Å)38.606, 38.606, 80.573
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 3045.993 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: 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: 2.72 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MGCL211
3SPERMINE11
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMDNA1drop
2200 mMcacodylate acid1drop
330 %(v/v)MPD1drop
47.8 mM1dropMgCl2
57.8 mMspermine1drop
6200 mMcacodylate acid1reservoir
730 %(v/v)MPD1reservoir

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Data collection

DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 5, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 4447 / % possible obs: 97 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.052
Reflection
*PLUS
Highest resolution: 1.7 Å / % possible obs: 97 % / Observed criterion σ(I): 3

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Processing

Software
NameClassification
X-PLORrefinement
XENGENdata reduction
RefinementResolution: 1.7→5 Å / σ(F): 2
RfactorNum. reflection
Rfree0.21 -
Rwork0.19 -
obs0.19 4447
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 227 0 156 383
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.64
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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_NDBX_HIGH.DNA / Topol file: TOP_NDBX.DNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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