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- PDB-1pnn: PEPTIDE NUCLEIC ACID (PNA) COMPLEXED WITH DNA -

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Basic information

Entry
Database: PDB / ID: 1pnn
TitlePEPTIDE NUCLEIC ACID (PNA) COMPLEXED WITH DNA
Components
  • DNA (5'-D(GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
  • PNA (NH2-P(*C*T*C*T*T*C*T*T*C-HIS-GLY-SER-SER-GLY-HIS-C*T*T*C*T*T*C*T*C)-COOH)
KeywordsPEPTIDE NUCLEIC ACID/DNA / HAIRPIN PNA:DNA TRIPLEX / TRIPLEX WATSON-CRICK HOOGSTEEN / PEPTIDE NUCLEIC ACID-DNA COMPLEX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsBetts, L. / Veal, J.M.
Citation
Journal: Science / Year: 1995
Title: A Nucleic Acid Triple Helix Formed by a Peptide Nucleic Acid-DNA Complex
Authors: Betts, L. / Josey, J.A. / Veal, J.M. / Jordan, S.R.
#1: Journal: Science / Year: 1994
Title: NMR Solution Structure of a Peptide Nucleic Acid Complexed with RNA
Authors: Brown, S.C. / Thomson, S.A. / Veal, J.M. / Davis, D.G.
History
DepositionOct 13, 1995Deposition site: NDB / Processing site: NDB
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PNA (NH2-P(*C*T*C*T*T*C*T*T*C-HIS-GLY-SER-SER-GLY-HIS-C*T*T*C*T*T*C*T*C)-COOH)
B: DNA (5'-D(GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
C: PNA (NH2-P(*C*T*C*T*T*C*T*T*C-HIS-GLY-SER-SER-GLY-HIS-C*T*T*C*T*T*C*T*C)-COOH)
D: DNA (5'-D(GP*AP*AP*GP*AP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)16,3204
Polymers16,3204
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.380, 73.380, 141.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.545117, -0.361267, -0.756527), (-0.305617, -0.754662, 0.580589), (-0.78067, 0.547697, 0.300969)
Vector: 55.7967, 73.526, 1.5171)

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Components

#1: DNA chain PNA (NH2-P(*C*T*C*T*T*C*T*T*C-HIS-GLY-SER-SER-GLY-HIS-C*T*T*C*T*T*C*T*C)-COOH) / HAIRPIN PNA:DNA TRIPLEX


Mass: 5322.071 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(GP*AP*AP*GP*AP*AP*GP*AP*G)-3')


Mass: 2837.900 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CRYSTALLIZED FROM AMMONIUM SULFATE AND TRIS PH 8.5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.978
ROTATING ANODE21.5418
Detector
TypeIDDetectorDate
1CCDMay 8, 1994
RIGAKU RAXIS IIC2IMAGE PLATEJan 11, 1994
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
21.54181
ReflectionResolution: 2.5→20 Å / Num. obs: 8374 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.043

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
RefinementResolution: 2.5→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.235 --
Rwork0.187 --
obs0.187 6857 95 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 380 0 35 1165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.43
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d6.75
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

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