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- PDB-401d: STRUCTURE OF A DNA IN LOW SALT CONDITIONS D(GACCGCGGTC) -

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Basic information

Entry
Database: PDB / ID: 401d
TitleSTRUCTURE OF A DNA IN LOW SALT CONDITIONS D(GACCGCGGTC)
ComponentsDNA (5'-D(*GP*AP*CP*CP*GP*CP*GP*GP*TP*C)-3')
KeywordsDNA / DNA DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 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
DepositionJun 2, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jul 6, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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
Water61334
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)38.444, 38.444, 80.175
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.: 34 / 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

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE_HCL11
4NA CACODYLATE11
5WATER12
6MPD12
Crystal grow
*PLUS
Details: This particular structure is not described in this paper.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41
51
61

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Data collection

DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 1811 / % possible obs: 82.3 % / Observed criterion σ(I): 3 / Redundancy: 6 % / Rmerge(I) obs: 0.039

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Processing

Software
NameClassification
X-PLORrefinement
SAINTdata reduction
SAINTdata scaling
RefinementResolution: 2.2→5 Å / Isotropic thermal model: ISOTROPIC / σ(F): 3
RfactorNum. reflection
Rfree0.285 -
Rwork0.219 -
obs0.219 1779
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 227 0 102 329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg0.81
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

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