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- PDB-1hzs: Crystal structure of a peptide nucleic acid duplex (BT-PNA) conta... -

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Basic information

Entry
Database: PDB / ID: 1hzs
TitleCrystal structure of a peptide nucleic acid duplex (BT-PNA) containing a bicyclic analogue of thymine
ComponentsPEPTIDE NUCLEIC ACID
KeywordsPEPTIDE NUCLEIC ACID / double helix / nucleobase analogue / P-form helix / left-handed / right-handed
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsEldrup, A.B. / Nielsen, B.B. / Haaima, G. / Rasmussen, H. / Kastrup, J.S. / Christensen, C. / Nielsen, P.E.
Citation
Journal: Eur.J.Org.Chem. / Year: 2001
Title: 1,8-Naphthyridin-2(1H)-ones. Novel Bicyclic and Tricyclic Analogues of Thymine in Peptide Nucleic Acids (PNAs)
Authors: Eldrup, A.B. / Nielsen, B.B. / Haaima, G. / Rasmussen, H. / Kastrup, J.S. / Christensen, C. / Nielsen, P.E.
#1: 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.
#2: Journal: New J.Chem. / Year: 1999
Title: Peptide Nucleic Acids (PNA) Derived from N-(N-methylaminoethyl)glycine. Synthesis, Hybridization and Structural Properties
Authors: Haima, G. / Rasmussen, H. / Schmidt, G. / Jensen, D.K. / Kastrup, J.S. / Stafshede, P.W. / Norden, B. / Buchardt, O. / Nielsen, P.E.
History
DepositionJan 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Remark 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). CHAINS A AND B BUILD A RIGHT-HANDED PNA DOUBLE HELIX AND CHAINS C AND D BUILD A LEFT-HANDED DOUBLE HELIX.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDE NUCLEIC ACID
B: PEPTIDE NUCLEIC ACID
C: PEPTIDE NUCLEIC ACID
D: PEPTIDE NUCLEIC ACID


Theoretical massNumber of molelcules
Total (without water)6,9354
Polymers6,9354
Non-polymers00
Water1,982110
1
A: PEPTIDE NUCLEIC ACID
B: PEPTIDE NUCLEIC ACID


Theoretical massNumber of molelcules
Total (without water)3,4682
Polymers3,4682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PEPTIDE NUCLEIC ACID
D: PEPTIDE NUCLEIC ACID


Theoretical massNumber of molelcules
Total (without water)3,4682
Polymers3,4682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.340, 45.000, 49.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsPNA double helix

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Components

#1: DNA chain
PEPTIDE NUCLEIC ACID


Mass: 1733.858 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthesized as described in the primary reference
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2-propanol, ammonium sulphate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
12-propanol11
2ammonium sulphate11
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.6 Mammonium sulfate1reservoir
35 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 18, 1999 / Details: segmental toroidal mirror
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.82→30 Å / Num. all: 6245 / Num. obs: 6233 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.1
Reflection shellResolution: 1.82→1.84 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.6 / Num. unique all: 169 / % possible all: 81.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PUP

1pup


Resolution: 1.82→6 Å / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 0 / Stereochemistry target values: own target values / Details: OWN PARAMETER AND TOPOLOGY FILE CREATED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 455 10 %random
Rwork0.208 ---
all-6024 --
obs-4196 --
Displacement parametersBiso mean: 16.2 Å2
Refinement stepCycle: LAST / Resolution: 1.82→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms516 0 0 110 626
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg3
LS refinement shellResolution: 1.82→1.9 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.266 41 10 %
Rwork0.241 281 -
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(F): 3 / % reflection Rfree: 10 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.269
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg3.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.266 / % reflection Rfree: 10 % / Rfactor Rwork: 0.241

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