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- PDB-231d: STRUCTURE OF A DNA-PORPHYRIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 231d
TitleSTRUCTURE OF A DNA-PORPHYRIN COMPLEX
ComponentsDNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / FLIPPED-OUT BASES / COMPLEXED WITH DRUG
Function / homologyCU(II)MESO(4-N-TETRAMETHYLPYRIDYL)PORPHYRIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsLipscomb, L.A. / Zhou, F.X. / Presnell, S.R. / Woo, R.J. / Peek, M.E. / Plaskon, R.R. / Williams, L.D.
CitationJournal: Biochemistry / Year: 1996
Title: Structure of DNA-porphyrin complex.
Authors: Lipscomb, L.A. / Zhou, F.X. / Presnell, S.R. / Woo, R.J. / Peek, M.E. / Plaskon, R.R. / Williams, L.D.
History
DepositionAug 25, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Mar 22, 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 / 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(*CP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5733
Polymers1,8091
Non-polymers7632
Water52229
1
A: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)5,1456
Polymers3,6182
Non-polymers1,5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_546x,x-y-1,-z+7/61
Unit cell
Length a, b, c (Å)39.490, 39.490, 56.150
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-8-

NA

21A-36-

HOH

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-PCU / CU(II)MESO(4-N-TETRAMETHYLPYRIDYL)PORPHYRIN


Mass: 740.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H36CuN8
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growMethod: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE_HCL11
5NA CACODYLATE11
6WATER12
7MPD12
8WATER13
9K2PTCL413
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMd(CGAT1CG)1drop
20.5 mMCuTMPyP41drop
30.5 %MPD1drop
41.0 mMmagnesium chloride1drop
50.5 mMspermine hydrochloride1drop
640.0 mMsodium cacodylate1drop
720 %1reservoir
81
91

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. all: 49552 / Num. obs: 1334

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.4→8 Å / σ(F): 1.5
RfactorNum. reflection% reflection
Rwork0.219 --
obs0.219 937 81.5 %
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 54 29 203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.16
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
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 1.5
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.51 Å / Total num. of bins used: 8 / Num. reflection obs: 87 / Rfactor obs: 0.255

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