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- PDB-1pup: CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 A... -

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Basic information

Entry
Database: PDB / ID: 1pup
TitleCRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION
ComponentsPNA (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-NH2)
KeywordsPEPTIDE NUCLEIC ACID / DNA ANALOGUE / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SIR / Resolution: 1.7 Å
AuthorsRasmussen, H. / Kastrup, J.S.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution.
Authors: Rasmussen, H. / Kastrup, J.S. / Nielsen, J.N. / Nielsen, J.M. / Nielsen, P.E.
#1: 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.
#2: Journal: Nat.Struct.Biol. / Year: 1996
Title: Solution Structure of a Petide Nucleic Acid-DNA Duplex
Authors: Eriksson, M. / Nielsen, P.E.
#3: 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
DepositionNov 1, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 25, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 28, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _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: PNA (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-NH2)
B: PNA (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-NH2)


Theoretical massNumber of molelcules
Total (without water)3,1712
Polymers3,1712
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.970, 26.920, 33.780
Angle α, β, γ (deg.)88.20, 79.40, 82.50
Int Tables number2
Space group name H-MP-1

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Components

#1: DNA chain PNA (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-NH2)


Mass: 1585.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Description: DERIVATIVE DATA WERE COLLECTED AT EMBL, HAMBURG AT BEAMLINE X31 TO 1.9 A RESOLUTION.
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NACL11
3MGCL211
4N(C16H33)(CH3)3BR11
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlPNA solution1drop
2300 mMsodium chloride1reservoir
310 mMmagnesium chloride1reservoir
41 mMcetyl trimethylammoniumbromide1reservoir

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 5222 / % possible obs: 77 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 7.3 / % possible all: 37
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 25 Å / % possible obs: 77 % / Redundancy: 1.9 %
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.9 Å / % possible obs: 37 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: SIR / Resolution: 1.7→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.25 530 10 %RANDOM
Rwork0.205 ---
all0.25 ---
obs0.205 5222 77 %-
Displacement parametersBiso mean: 11.7 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms236 0 0 82 318
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.6
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_d0.73
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
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.184 21 10 %
Rwork0.285 182 -
obs--25 %
Xplor fileSerial no: 1 / Param file: PARAM.PNA / Topol file: TOPH_JULY96.PNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.285

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