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- PDB-1rru: The influence of a chiral amino acid on the helical handedness of... -

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Basic information

Entry
Database: PDB / ID: 1rru
TitleThe influence of a chiral amino acid on the helical handedness of PNA in solution and in crystals
ComponentsPeptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)
KeywordsPEPTIDE NUCLEIC ACID / PNA / L-Lysine / helical handedness / P-form / molecular mechanics
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRasmussen, H. / Liljefors, T. / Petersson, B. / Nielsen, P.E. / Kastrup, J.S.
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 2004
Title: The Influence of a Chiral Amino Acid on the Helical Handedness of PNA in Solution and in Crystals
Authors: Rasmussen, H. / Liljefors, T. / Petersson, B. / Nielsen, P.E. / Kastrup, J.S.
#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: Haiima, G. / Rasmussen, H. / Schmidt, G. / Jensen, D.K. / Kastrup, J.S. / Stafshede, P.W. / Norden, B. / Buckhardt, O. / Nielsen, P.E.
#3: Journal: Eur.J.Org.Chem. / Year: 2001
Title: 1,8-Naphthyridin-2(1H)-ones. Novel bi- and tricyclic analogues of Thymine in Peptide nucleic acids (PNA)
Authors: Eldrup, A.B. / Nielsen, B.B. / Haiima, G. / Rasmussen, H. / Kastrup, J.S. / Christensen, C. / Nielsen, P.E.
History
DepositionDec 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 28, 2019Group: Data collection / Derived calculations
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_biol / struct_conn
Revision 1.4Aug 23, 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)
B: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)


Theoretical massNumber of molelcules
Total (without water)3,4302
Polymers3,4302
Non-polymers00
Water50428
1
A: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)

A: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)


Theoretical massNumber of molelcules
Total (without water)3,4302
Polymers3,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)

B: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)


Theoretical massNumber of molelcules
Total (without water)3,4302
Polymers3,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)36.75, 44.07, 31.22
Angle α, β, γ (deg.)90.00, 91.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2) / / PNA


Mass: 1714.813 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: glycerol, magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1glycerol11
2magnesium formate11
3H2O11
4magnesium formate12
5H2O12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 16, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. all: 2069 / Num. obs: 2069 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.2 / Num. unique all: 92 / % possible all: 95.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
X-PLOR3.851refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PUP

1pup


Resolution: 2.35→6 Å / Isotropic thermal model: isotropic / Cross valid method: troughout / σ(F): 3 / Stereochemistry target values: Engh & Huber / Details: Own parameter and topology file created
RfactorNum. reflection% reflectionSelection details
Rfree0.292 129 -random
Rwork0.219 ---
all-1955 --
obs-1453 74 %-
Displacement parametersBiso mean: 38.4 Å2
Refinement stepCycle: LAST / Resolution: 2.35→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms254 0 0 28 282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
X-RAY DIFFRACTIONx_angle_deg3.5
LS refinement shellResolution: 2.35→2.45 Å /
RfactorNum. reflection
Rfree0.366 15
Rwork0.321 -

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